| Year |
Citation |
Score |
| 2021 |
Sieradzan AK, Korneev A, Begun A, Kachlishvili K, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 33909430 DOI: 10.1021/acs.jctc.1c00155 |
0.795 |
|
| 2020 |
Rackovsky S, Scheraga HA. The structure of protein dynamic space. Proceedings of the National Academy of Sciences of the United States of America. PMID 32759212 DOI: 10.1073/Pnas.2008873117 |
0.359 |
|
| 2020 |
Grassein P, Delarue P, Nicolaï A, Neiers F, Scheraga HA, Maisuradze GG, Senet P. Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding. The Journal of Physical Chemistry. B. PMID 32392067 DOI: 10.1021/Acs.Jpcb.0C01230 |
0.368 |
|
| 2020 |
Kachlishvili K, Korneev A, Maisuradze L, Liu J, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. New Insights into Folding, Misfolding and Nonfolding Dynamics of a WW Domain. The Journal of Physical Chemistry. B. PMID 32271570 DOI: 10.1021/Acs.Jpcb.0C00628 |
0.81 |
|
| 2020 |
Hwang S, Lee CJ, Lee S, Ma S, Kang YM, Cho KH, Kim SY, Kwon OY, Yoon CN, Kang YK, Yoon JH, Nam KY, Kim SG, In Y, Chai HH, ... ... Scheraga HA, et al. Development of a Physics-Based Molecular Force Field for Biomolecule Simulations. The Journal of Physical Chemistry. B. PMID 31939671 DOI: 10.1021/Acs.Jpcb.9B10339 |
0.542 |
|
| 2020 |
Arroyuelo A, Martin OA, Scheraga HA, Vila JA. Assessing the One-Bond C-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches. The Journal of Physical Chemistry. B. PMID 31928007 DOI: 10.1021/Acs.Jpcb.9B10123 |
0.304 |
|
| 2019 |
Scheraga HA, Rackovsky S. Sequence-specific dynamic information in proteins. Proteins. 87: 799-804. PMID 31134683 DOI: 10.1002/Prot.25747 |
0.35 |
|
| 2019 |
Martin OA, Vorobjev Y, Scheraga HA, Vila JA. Outline of an experimental design aimed to detect protein A mirror image in solution Peerj Physical Chemistry. 1: e2. DOI: 10.7717/Peerj-Pchem.2 |
0.324 |
|
| 2018 |
Sieradzan AK, Giełdoń A, Yin Y, He Y, Scheraga HA, Liwo A. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. Journal of Computational Chemistry. PMID 30306573 DOI: 10.1002/Jcc.25571 |
0.475 |
|
| 2018 |
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Scheraga H, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8 |
0.317 |
|
| 2018 |
Cote Y, Delarue P, Scheraga HA, Senet P, Maisuradze GG. From a highly-disordered to a metastable state: Uncovering insights of α-synuclein. Acs Chemical Neuroscience. PMID 29451381 DOI: 10.1021/Acschemneuro.7B00446 |
0.339 |
|
| 2018 |
Grassein P, Delarue P, Scheraga HA, Maisuradze GG, Senet P. Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale. The Journal of Physical Chemistry. B. PMID 29446945 DOI: 10.1021/Acs.Jpcb.7B10733 |
0.37 |
|
| 2018 |
Solé-Domènech S, Rojas AV, Maisuradze GG, Scheraga HA, Lobel P, Maxfield FR. Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain. Proceedings of the National Academy of Sciences of the United States of America. PMID 29378960 DOI: 10.1073/Pnas.1719808115 |
0.515 |
|
| 2017 |
Krupa P, Sieradzan AK, Mozolewska MA, Li H, Liwo A, Scheraga HA. Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A. Journal of Chemical Theory and Computation. PMID 28942648 DOI: 10.1021/Acs.Jctc.7B00724 |
0.375 |
|
| 2017 |
Vorobjev YN, Scheraga HA, Vila JA. A comprehensive Analysis of the Computed Tautomer Fractions of the Imidazole Ring of Histidines in Loligo vulgaris. Journal of Biomolecular Structure & Dynamics. 1-29. PMID 28884632 DOI: 10.1080/07391102.2017.1377636 |
0.388 |
|
| 2017 |
Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. Journal of Chemical Information and Modeling. PMID 28809487 DOI: 10.1021/Acs.Jcim.7B00254 |
0.326 |
|
| 2017 |
He Y, Maisuradze GG, Yin Y, Kachlishvili K, Rackovsky S, Scheraga HA. Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 28143938 DOI: 10.1073/Pnas.1621344114 |
0.798 |
|
| 2017 |
Vorobjev YN, Scheraga HA, Vila JA. Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins. Journal of Biomolecular Structure & Dynamics. 1-52. PMID 28132613 DOI: 10.1080/07391102.2017.1288169 |
0.378 |
|
| 2017 |
Rojas A, Maisuradze N, Kachlishvili K, Scheraga HA, Maisuradze GG. Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics. Acs Chemical Neuroscience. 8: 201-209. PMID 28095675 DOI: 10.1021/Acschemneuro.6B00331 |
0.795 |
|
| 2017 |
Makowski M, Liwo A, Scheraga HA. Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. The Journal of Physical Chemistry. B. PMID 28000446 DOI: 10.1021/Acs.Jpcb.6B08541 |
0.355 |
|
| 2016 |
Kachlishvili K, Dave K, Gruebele M, Scheraga HA, Maisuradze GG. Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic Contact. The Journal of Physical Chemistry. B. PMID 27584585 DOI: 10.1021/Acs.Jpcb.6B07250 |
0.802 |
|
| 2016 |
Garay PG, Martin OA, Scheraga HA, Vila JA. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. Peerj. 4: e2253. PMID 27547559 DOI: 10.7717/Peerj.2253 |
0.326 |
|
| 2016 |
Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczyńska A, Ślusarz M, Ślusarz R, Giełdoń A, Czaplewski C, Jagieła D, Zaborowski B, ... Scheraga HA, et al. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics (Oxford, England). PMID 27378298 DOI: 10.1093/Bioinformatics/Btw404 |
0.484 |
|
| 2016 |
Lipska AG, Seidman SR, Sieradzan AK, Giełdoń A, Liwo A, Scheraga HA. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. The Journal of Chemical Physics. 144: 184110. PMID 27179474 DOI: 10.1063/1.4948710 |
0.407 |
|
| 2016 |
Scheraga HA, Rackovsky S. Global informatics and physical property selection in protein sequences. Proceedings of the National Academy of Sciences of the United States of America. PMID 26831093 DOI: 10.1073/Pnas.1525745113 |
0.743 |
|
| 2015 |
He Y, Liwo A, Scheraga HA. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. The Journal of Chemical Physics. 143: 243111. PMID 26723596 DOI: 10.1063/1.4932082 |
0.431 |
|
| 2015 |
Maisuradze GG, Medina J, Kachlishvili K, Krupa P, Mozolewska MA, Martin-Malpartida P, Maisuradze L, Macias MJ, Scheraga HA. Preventing fibril formation of a protein by selective mutation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26483482 DOI: 10.1073/Pnas.1518298112 |
0.81 |
|
| 2015 |
Wiśniewska M, Sobolewski E, Ołdziej S, Liwo A, Scheraga HA, Makowski M. Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water. The Journal of Physical Chemistry. B. 119: 8526-34. PMID 26100791 DOI: 10.1021/Acs.Jpcb.5B04782 |
0.348 |
|
| 2015 |
Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. Physics-based potentials for coarse-grained modeling of protein-DNA interactions. Journal of Chemical Theory and Computation. 11: 1792-1808. PMID 26052263 DOI: 10.1021/Ct5009558 |
0.442 |
|
| 2015 |
Mozolewska MA, Krupa P, Scheraga HA, Liwo A. Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches. Proteins. 83: 1414-26. PMID 25973573 DOI: 10.1002/Prot.24824 |
0.335 |
|
| 2015 |
Cote Y, Maisuradze GG, Delarue P, Scheraga HA, Senet P. New Insights into Protein (Un)Folding Dynamics. The Journal of Physical Chemistry Letters. 6: 1082-1086. PMID 25866611 DOI: 10.1021/Acs.Jpclett.5B00055 |
0.382 |
|
| 2015 |
Scheraga HA. My 65 years in protein chemistry. Quarterly Reviews of Biophysics. 48: 117-77. PMID 25850343 DOI: 10.1017/S0033583514000134 |
0.305 |
|
| 2015 |
He Y, Rackovsky S, Yin Y, Scheraga HA. Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proceedings of the National Academy of Sciences of the United States of America. 112: 5029-32. PMID 25848034 DOI: 10.1073/Pnas.1504806112 |
0.772 |
|
| 2015 |
Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations. Journal of Chemical Theory and Computation. 11: 817-831. PMID 25691834 DOI: 10.1021/Ct500736A |
0.435 |
|
| 2015 |
Go?a? EI, Czaplewski C, Scheraga HA, Liwo A. Common functionally important motions of the nucleotide-binding domain of Hsp70. Proteins. 83: 282-99. PMID 25412765 DOI: 10.1002/Prot.24731 |
0.31 |
|
| 2015 |
He Y, Liwo A, Scheraga HA. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach Journal of Chemical Physics. 143. DOI: 10.1063/1.4932082 |
0.305 |
|
| 2015 |
Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. Physics-based potentials for coarse-grained modeling of protein-DNA interactions Journal of Chemical Theory and Computation. 11: 1792-1808. DOI: 10.1021/ct5009558 |
0.303 |
|
| 2014 |
Zhou R, Maisuradze GG, Suñol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proceedings of the National Academy of Sciences of the United States of America. 111: 18243-8. PMID 25489078 DOI: 10.1073/Pnas.1420914111 |
0.369 |
|
| 2014 |
Maciejczyk M, Spasic A, Liwo A, Scheraga HA. DNA Duplex Formation with a Coarse-Grained Model. Journal of Chemical Theory and Computation. 10: 5020-5035. PMID 25400520 DOI: 10.1021/Ct4006689 |
0.353 |
|
| 2014 |
Garay PG, Martin OA, Scheraga HA, Vila JA. Factors affecting the computation of the 13C shielding in disaccharides. Journal of Computational Chemistry. 35: 1854-64. PMID 25066622 DOI: 10.1002/Jcc.23697 |
0.338 |
|
| 2014 |
Liwo A, Baranowski M, Czaplewski C, Go?a? E, He Y, Jagie?a D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, O?dziej S, Scheraga HA, Sieradzan AK, Slusarz R, et al. A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. Journal of Molecular Modeling. 20: 2306. PMID 25024008 DOI: 10.1007/S00894-014-2306-5 |
0.465 |
|
| 2014 |
Kachlishvili K, Maisuradze GG, Martin OA, Liwo A, Vila JA, Scheraga HA. Accounting for a mirror-image conformation as a subtle effect in protein folding. Proceedings of the National Academy of Sciences of the United States of America. 111: 8458-63. PMID 24912167 DOI: 10.1073/Pnas.1407837111 |
0.814 |
|
| 2014 |
Sieradzan AK, Niadzvedtski A, Scheraga HA, Liwo A. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field. Journal of Chemical Theory and Computation. 10: 2194-2203. PMID 24839411 DOI: 10.1021/Ct500119R |
0.406 |
|
| 2014 |
Scheraga HA, Rackovsky S. Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. Proceedings of the National Academy of Sciences of the United States of America. 111: 5225-9. PMID 24706836 DOI: 10.1073/Pnas.1403599111 |
0.767 |
|
| 2014 |
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, ... ... Scheraga HA, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/Prot.24538 |
0.433 |
|
| 2014 |
Krokhotin A, Liwo A, Maisuradze GG, Niemi AJ, Scheraga HA. Kinks, loops, and protein folding, with protein A as an example. The Journal of Chemical Physics. 140: 025101. PMID 24437917 DOI: 10.1063/1.4855735 |
0.427 |
|
| 2014 |
Vila JA, Arnautova YA, Martin OA, Scheraga HA. Are accurate computations of the 13C' shielding feasible at the DFT level of theory? Journal of Computational Chemistry. 35: 309-12. PMID 24403017 DOI: 10.1002/Jcc.23499 |
0.372 |
|
| 2014 |
Liwo JA, Sieradzan AK, He Y, Krupa P, Czaplewski CR, Krokhotin A, Niemi AJ, Scheraga HA. Origin of the Architecture of Biological Macromolecules - A Mean-Field Perspective Biophysical Journal. 106: 256a. DOI: 10.1016/J.Bpj.2013.11.1506 |
0.47 |
|
| 2013 |
Krupa P, Sieradzan AK, Rackovsky S, Baranowski M, O?ldziej S, Scheraga HA, Liwo A, Czaplewski C. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. Journal of Chemical Theory and Computation. 9. PMID 24273465 DOI: 10.1021/Ct4004977 |
0.798 |
|
| 2013 |
Martin OA, Arnautova YA, Icazatti AA, Scheraga HA, Vila JA. Physics-based method to validate and repair flaws in protein structures. Proceedings of the National Academy of Sciences of the United States of America. 110: 16826-31. PMID 24082119 DOI: 10.1073/Pnas.1315525110 |
0.395 |
|
| 2013 |
He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Åšlusarz R, Czaplewski CR, OÅ‚dziej S, Scheraga HA. Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proceedings of the National Academy of Sciences of the United States of America. 110: 14936-41. PMID 23980156 DOI: 10.1073/Pnas.1313316110 |
0.787 |
|
| 2013 |
Maisuradze GG, Liwo A, Senet P, Scheraga HA. Local vs global motions in protein folding. Journal of Chemical Theory and Computation. 9: 2907-2921. PMID 23914144 DOI: 10.1021/Ct4001558 |
0.42 |
|
| 2013 |
He Y, Maciejczyk M, OÅ‚dziej S, Scheraga HA, Liwo A. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Physical Review Letters. 110: 098101. PMID 23496746 DOI: 10.1103/Physrevlett.110.098101 |
0.462 |
|
| 2013 |
Lee S, Cho KH, Kang YM, Scheraga HA, No KT. A generalized G-SFED continuum solvation free energy calculation model. Proceedings of the National Academy of Sciences of the United States of America. 110: E662-7. PMID 23378634 DOI: 10.1073/Pnas.1221940110 |
0.507 |
|
| 2013 |
Lam AR, Rodriguez JJ, Rojas A, Scheraga HA, Mukamel S. Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy. The Journal of Physical Chemistry. A. 117: 342-50. PMID 23214934 DOI: 10.1021/Jp3101267 |
0.311 |
|
| 2012 |
Sieradzan AK, Hansmann UH, Scheraga HA, Liwo A. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. Journal of Chemical Theory and Computation. 8: 4746-4757. PMID 24729761 DOI: 10.1021/Ct3005563 |
0.401 |
|
| 2012 |
Sieradzan AK, Scheraga HA, Liwo A. Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. Journal of Chemical Theory and Computation. 8: 1334-1343. PMID 23087598 DOI: 10.1021/Ct2008439 |
0.359 |
|
| 2012 |
Krokhotin A, Liwo A, Niemi AJ, Scheraga HA. Coexistence of phases in a protein heterodimer. The Journal of Chemical Physics. 137: 035101. PMID 22830730 DOI: 10.1063/1.4734019 |
0.341 |
|
| 2012 |
Go?a? E, Maisuradze GG, Senet P, O?dziej S, Czaplewski C, Scheraga HA, Liwo A. Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. Journal of Chemical Theory and Computation. 8: 1750-1764. PMID 22737044 DOI: 10.1021/Ct200680G |
0.345 |
|
| 2012 |
Yin Y, Maisuradze GG, Liwo A, Scheraga HA. Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. Journal of Chemical Theory and Computation. 8: 1176-1189. PMID 22715321 DOI: 10.1021/Ct200806N |
0.398 |
|
| 2012 |
Cote Y, Senet P, Delarue P, Maisuradze GG, Scheraga HA. Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proceedings of the National Academy of Sciences of the United States of America. 109: 10346-51. PMID 22689963 DOI: 10.1073/Pnas.1207083109 |
0.331 |
|
| 2012 |
Maisuradze GG, Zhou R, Liwo A, Xiao Y, Scheraga HA. Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. Journal of Molecular Biology. 420: 350-65. PMID 22560992 DOI: 10.1016/J.Jmb.2012.04.027 |
0.36 |
|
| 2012 |
Martin OA, Vila JA, Scheraga HA. CheShift-2: graphic validation of protein structures. Bioinformatics (Oxford, England). 28: 1538-9. PMID 22495749 DOI: 10.1093/Bioinformatics/Bts179 |
0.367 |
|
| 2012 |
Makowska J, Liwo A, Zmudzińska W, Lewandowska A, Chmurzyński L, Scheraga HA. Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal. Biopolymers. 97: 240-9. PMID 22161955 DOI: 10.1002/Bip.22013 |
0.335 |
|
| 2012 |
Gahl RF, Oswald RE, Scheraga HA. Identification of formation of initial native structure in onconase from an unfolded state. Biochemistry. 51: 521-32. PMID 22142378 DOI: 10.1021/Bi201168D |
0.384 |
|
| 2012 |
Lam AR, Jiang J, Rojas A, Scheraga H, Mukamel S. Monitoring the Mechanism of Fiber Assembly of AB Peptides in Alzheimer's Disease (AD) by Two-Dimensional Ultraviolet (2DUV) Spectroscopy Biophysical Journal. 102: 733a. DOI: 10.1016/J.Bpj.2011.11.3977 |
0.301 |
|
| 2011 |
Rojas AV, Liwo A, Scheraga HA. A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)). The Journal of Physical Chemistry. B. 115: 12978-83. PMID 21939202 DOI: 10.1021/Jp2050993 |
0.381 |
|
| 2011 |
Liwo A, He Y, Scheraga HA. Coarse-grained force field: general folding theory. Physical Chemistry Chemical Physics : Pccp. 13: 16890-901. PMID 21643583 DOI: 10.1039/C1Cp20752K |
0.493 |
|
| 2011 |
Makowski M, Liwo A, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. The Journal of Physical Chemistry. B. 115: 6130-7. PMID 21500791 DOI: 10.1021/Jp111259E |
0.321 |
|
| 2011 |
Vila JA, Arnautova YA, Vorobjev Y, Scheraga HA. Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proceedings of the National Academy of Sciences of the United States of America. 108: 5602-7. PMID 21422292 DOI: 10.1073/Pnas.1102373108 |
0.371 |
|
| 2011 |
Rackovsky S, Scheraga HA. On the information content of protein sequences. Journal of Biomolecular Structure & Dynamics. 28: 593-4; discussion 66. PMID 21142228 DOI: 10.1080/073911011010524957 |
0.724 |
|
| 2011 |
He Y, Liwo A, Weinstein H, Scheraga HA. PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. Journal of Molecular Biology. 405: 298-314. PMID 21050858 DOI: 10.1016/J.Jmb.2010.10.051 |
0.419 |
|
| 2010 |
Maisuradze GG, Liwo A, Scheraga HA. Relation between free energy landscapes of proteins and dynamics. Journal of Chemical Theory and Computation. 6: 583-595. PMID 23620713 DOI: 10.1021/Ct9005745 |
0.366 |
|
| 2010 |
Cote Y, Senet P, Delarue P, Maisuradze GG, Scheraga HA. Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations. Proceedings of the National Academy of Sciences of the United States of America. 107: 19844-9. PMID 21045133 DOI: 10.1073/Pnas.1013674107 |
0.356 |
|
| 2010 |
Rojas A, Liwo A, Browne D, Scheraga HA. Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. Journal of Molecular Biology. 404: 537-52. PMID 20888834 DOI: 10.1016/J.Jmb.2010.09.057 |
0.399 |
|
| 2010 |
Vila JA, Serrano P, Wüthrich K, Scheraga HA. Sequential nearest-neighbor effects on computed 13Calpha chemical shifts. Journal of Biomolecular Nmr. 48: 23-30. PMID 20644980 DOI: 10.1007/S10858-010-9435-7 |
0.54 |
|
| 2010 |
Maisuradze GG, Liwo A, OÅ‚dziej S, Scheraga HA. Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. Journal of the American Chemical Society. 132: 9444-52. PMID 20568747 DOI: 10.1021/Ja1031503 |
0.387 |
|
| 2010 |
Lewandowska A, OÅ‚dziej S, Liwo A, Scheraga HA. beta-hairpin-forming peptides; models of early stages of protein folding. Biophysical Chemistry. 151: 1-9. PMID 20494507 DOI: 10.1016/J.Bpc.2010.05.001 |
0.41 |
|
| 2010 |
Liwo A, O?dziej S, Czaplewski C, Kleinerman DS, Blood P, Scheraga HA. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. Journal of Chemical Theory and Computation. 6: 890-909. PMID 20305729 DOI: 10.1021/Ct9004068 |
0.336 |
|
| 2010 |
Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. The Journal of Physical Chemistry. A. 114: 4471-85. PMID 20166738 DOI: 10.1021/Jp9117776 |
0.419 |
|
| 2010 |
Martin OA, Villegas ME, Vila JA, Scheraga HA. Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach. Journal of Biomolecular Nmr. 46: 217-25. PMID 20091207 DOI: 10.1007/S10858-010-9396-X |
0.388 |
|
| 2010 |
Kozłowska U, Liwo A, Scheraga HA. Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method. Journal of Computational Chemistry. 31: 1143-53. PMID 20073062 DOI: 10.1002/Jcc.21399 |
0.423 |
|
| 2010 |
Lewandowska A, OÅ‚dziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein. Biopolymers. 93: 469-80. PMID 20049918 DOI: 10.1002/Bip.21365 |
0.376 |
|
| 2010 |
Makowski M, Czaplewski C, Liwo A, Scheraga HA. Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit. The Journal of Physical Chemistry. B. 114: 993-1003. PMID 20039620 DOI: 10.1021/Jp907794H |
0.318 |
|
| 2010 |
Maciejczyk M, Spasic A, Liwo A, Scheraga HA. Coarse-grained model of nucleic acid bases. Journal of Computational Chemistry. 31: 1644-55. PMID 20020472 DOI: 10.1002/Jcc.21448 |
0.314 |
|
| 2010 |
Kozłowska U, Maisuradze GG, Liwo A, Scheraga HA. Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. Journal of Computational Chemistry. 31: 1154-67. PMID 20017135 DOI: 10.1002/Jcc.21402 |
0.445 |
|
| 2010 |
Lewandowska A, OÅ‚dziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions. Proteins. 78: 723-37. PMID 19847914 DOI: 10.1002/Prot.22605 |
0.373 |
|
| 2010 |
Fitzwater S, Scheraga HA. Combined-information protein structure refinement: Potential energy-constrained real-space method for refinement with limited diffraction data. Proceedings of the National Academy of Sciences of the United States of America. 79: 2133-7. PMID 16593175 DOI: 10.1073/Pnas.79.6.2133 |
0.338 |
|
| 2010 |
Shipman LL, Burgess AW, Scheraga HA. A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proceedings of the National Academy of Sciences of the United States of America. 72: 543-7. PMID 16592221 DOI: 10.1073/Pnas.72.2.543 |
0.335 |
|
| 2010 |
Rasse D, Warme PK, Scheraga HA. Refinement of the X-ray Structure of Rubredoxin by Conformational Energy Calculations. Proceedings of the National Academy of Sciences of the United States of America. 71: 3736-40. PMID 16592180 DOI: 10.1073/Pnas.71.9.3736 |
0.389 |
|
| 2010 |
Scott RA, Vanderkooi G, Tuttle RW, Shames PM, Scheraga HA. Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s. Proceedings of the National Academy of Sciences of the United States of America. 58: 2204-11. PMID 16591582 DOI: 10.1073/Pnas.58.6.2204 |
0.317 |
|
| 2009 |
Czaplewski C, Kalinowski S, Liwo A, Scheraga HA. Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. Journal of Chemical Theory and Computation. 5: 627-640. PMID 20161452 DOI: 10.1021/Ct800397Z |
0.302 |
|
| 2009 |
Jang SH, Song HD, Kang DK, Chang SI, Kim MK, Cho KH, Scheraga HA, Shin HC. Role of the surface loop on the structure and biological activity of angiogenin. Bmb Reports. 42: 829-33. PMID 20044956 DOI: 10.5483/Bmbrep.2009.42.12.829 |
0.499 |
|
| 2009 |
Vila JA, Arnautova YA, Martin OA, Scheraga HA. Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proceedings of the National Academy of Sciences of the United States of America. 106: 16972-7. PMID 19805131 DOI: 10.1073/Pnas.0908833106 |
0.38 |
|
| 2009 |
Maisuradze GG, Liwo A, Scheraga HA. How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics? Physical Review Letters. 102: 238102. PMID 19658975 DOI: 10.1103/Physrevlett.102.238102 |
0.372 |
|
| 2009 |
Vila JA, Scheraga HA. Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Accounts of Chemical Research. 42: 1545-53. PMID 19572703 DOI: 10.1021/Ar900068S |
0.391 |
|
| 2009 |
Arnautova YA, Vila JA, Martin OA, Scheraga HA. What can we learn by computing 13Calpha chemical shifts for X-ray protein models? Acta Crystallographica. Section D, Biological Crystallography. 65: 697-703. PMID 19564690 DOI: 10.1107/S0907444909012086 |
0.346 |
|
| 2009 |
Shen H, Liwo A, Scheraga HA. An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics. The Journal of Physical Chemistry. B. 113: 8738-44. PMID 19480420 DOI: 10.1021/Jp901788Q |
0.331 |
|
| 2009 |
Arnautova YA, Vorobjev YN, Vila JA, Scheraga HA. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Proteins. 77: 38-51. PMID 19384995 DOI: 10.1002/Prot.22414 |
0.392 |
|
| 2009 |
Gahl RF, Pradeep L, Siegel CR, Xu G, Scheraga HA. Effects of tyrosine mutations on the conformational and oxidative folding of ribonuclease a: a comparative study. Biochemistry. 48: 3887-93. PMID 19344116 DOI: 10.1021/Bi802362T |
0.407 |
|
| 2009 |
Gahl RF, Scheraga HA. Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues. Biochemistry. 48: 2740-51. PMID 19309163 DOI: 10.1021/Bi802327J |
0.329 |
|
| 2009 |
He Y, Xiao Y, Liwo A, Scheraga HA. Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. Journal of Computational Chemistry. 30: 2127-35. PMID 19242966 DOI: 10.1002/Jcc.21215 |
0.478 |
|
| 2009 |
Skwierawska A, Zmudzińska W, Ołdziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation. Proteins. 76: 637-54. PMID 19241469 DOI: 10.1002/Prot.22377 |
0.379 |
|
| 2009 |
Skwierawska A, Makowska J, OÅ‚dziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure. Proteins. 75: 931-53. PMID 19089955 DOI: 10.1002/Prot.22304 |
0.397 |
|
| 2009 |
Maisuradze GG, Liwo A, Scheraga HA. Principal component analysis for protein folding dynamics. Journal of Molecular Biology. 385: 312-29. PMID 18952103 DOI: 10.1016/J.Jmb.2008.10.018 |
0.363 |
|
| 2009 |
Vila JA, Baldoni HA, Scheraga HA. Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. Journal of Computational Chemistry. 30: 884-92. PMID 18780343 DOI: 10.1002/Jcc.21105 |
0.363 |
|
| 2009 |
Skwierawska A, OÅ‚dziej S, Liwo A, Scheraga HA. Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers. 91: 37-51. PMID 18767128 DOI: 10.1002/Bip.21080 |
0.377 |
|
| 2009 |
NAIK V, KRIMM S, DENTON J, NÉMETHY G, SCHERAGA H. Vibrational analysis of peptides, polypeptides and proteins International Journal of Peptide and Protein Research. 24: 613-626. DOI: 10.1111/j.1399-3011.1984.tb03168.x |
0.681 |
|
| 2009 |
PATERSON Y, STIMSON ER, EVANS DJ, LEACH SJ, SCHERAGA HA. Solution conformations of oligomers of α -aminoisobutyric acid° International Journal of Peptide and Protein Research. 20: 468-480. DOI: 10.1111/J.1399-3011.1982.Tb03069.X |
0.364 |
|
| 2008 |
Senet P, Maisuradze GG, Foulie C, Delarue P, Scheraga HA. How main-chains of proteins explore the free-energy landscape in native states. Proceedings of the National Academy of Sciences of the United States of America. 105: 19708-13. PMID 19073932 DOI: 10.1073/Pnas.0810679105 |
0.385 |
|
| 2008 |
Vila JA, Aramini JM, Rossi P, Kuzin A, Su M, Seetharaman J, Xiao R, Tong L, Montelione GT, Scheraga HA. Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proceedings of the National Academy of Sciences of the United States of America. 105: 14389-94. PMID 18787110 DOI: 10.1073/Pnas.0807105105 |
0.525 |
|
| 2008 |
Makowska J, Bagińska K, Skwierawska A, Liwo A, Chmurzyński L, Scheraga HA. Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides. Biopolymers. 90: 772-82. PMID 18767125 DOI: 10.1002/Bip.21077 |
0.386 |
|
| 2008 |
Makowski M, Sobolewski E, Czaplewski C, OÅ‚dziej S, Liwo A, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. The Journal of Physical Chemistry. B. 112: 11385-95. PMID 18700740 DOI: 10.1021/Jp803896B |
0.411 |
|
| 2008 |
Vorobjev YN, Vila JA, Scheraga HA. FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins. The Journal of Physical Chemistry. B. 112: 11122-36. PMID 18683966 DOI: 10.1021/Jp709969N |
0.347 |
|
| 2008 |
Skwierawska A, Rodziewicz-Motowidło S, Ołdziej S, Liwo A, Scheraga HA. Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers. 89: 1032-44. PMID 18655142 DOI: 10.1002/Bip.21056 |
0.371 |
|
| 2008 |
Makowska J, Bagińska K, Liwo A, Chmurzyński L, Scheraga HA. Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment. Biopolymers. 90: 724-32. PMID 18618612 DOI: 10.1002/Bip.21046 |
0.345 |
|
| 2008 |
Arnautova YA, Scheraga HA. Use of decoys to optimize an all-atom force field including hydration. Biophysical Journal. 95: 2434-49. PMID 18502794 DOI: 10.1529/Biophysj.108.133587 |
0.337 |
|
| 2008 |
Kang YK, Scheraga HA. An efficient method for calculating atomic charges of peptides and proteins from electronic populations. The Journal of Physical Chemistry. B. 112: 5470-8. PMID 18399682 DOI: 10.1021/Jp711484F |
0.313 |
|
| 2008 |
Narayan M, Welker E, Zhai H, Han X, Xu G, McLafferty FW, Scheraga HA. Detecting native folds in mixtures of proteins that contain disulfide bonds. Nature Biotechnology. 26: 427-9. PMID 18278035 DOI: 10.1038/Nbt1380 |
0.565 |
|
| 2008 |
Vila JA, Arnautova YA, Scheraga HA. Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution. Proceedings of the National Academy of Sciences of the United States of America. 105: 1891-6. PMID 18250334 DOI: 10.1073/Pnas.0711022105 |
0.406 |
|
| 2008 |
Gahl RF, Narayan M, Xu G, Scheraga HA. Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues. Protein Engineering, Design & Selection : Peds. 21: 223-31. PMID 18245105 DOI: 10.1093/Protein/Gzm093 |
0.558 |
|
| 2008 |
Liwo A, Czaplewski C, OÅ‚dziej S, Scheraga HA. Computational techniques for efficient conformational sampling of proteins. Current Opinion in Structural Biology. 18: 134-9. PMID 18215513 DOI: 10.1016/J.Sbi.2007.12.001 |
0.353 |
|
| 2008 |
Scheraga HA. From helix-coil transitions to protein folding. Biopolymers. 89: 479-85. PMID 18008324 DOI: 10.1002/Bip.20890 |
0.422 |
|
| 2008 |
Vila JA, Scheraga HA. Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins. 71: 641-54. PMID 17975838 DOI: 10.1002/Prot.21726 |
0.391 |
|
| 2008 |
Chen J, Brooks CL, Scheraga HA. Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. The Journal of Physical Chemistry. B. 112: 242-9. PMID 17880128 DOI: 10.1021/Jp074355H |
0.406 |
|
| 2007 |
Chinchio M, Czaplewski C, Liwo A, Ołdziej S, Scheraga HA. Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field. Journal of Chemical Theory and Computation. 3: 1236-48. PMID 26633198 DOI: 10.1021/ct7000842 |
0.807 |
|
| 2007 |
Murarka RK, Liwo A, Scheraga HA. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone. The Journal of Chemical Physics. 127: 155103. PMID 17949219 DOI: 10.1063/1.2784200 |
0.724 |
|
| 2007 |
Pradeep L, Kurinov I, Ealick SE, Scheraga HA. Implementation of a k/k(0) method to identify long-range structure in transition states during conformational folding/unfolding of proteins. Structure (London, England : 1993). 15: 1178-89. PMID 17937908 DOI: 10.1016/J.Str.2007.08.003 |
0.37 |
|
| 2007 |
Sobolewski E, Makowski M, Czaplewski C, Liwo A, OÅ‚dziej S, Scheraga HA. Potential of mean force of hydrophobic association: dependence on solute size. The Journal of Physical Chemistry. B. 111: 10765-74. PMID 17713937 DOI: 10.1021/Jp070594T |
0.316 |
|
| 2007 |
Vila JA, Villegas ME, Baldoni HA, Scheraga HA. Predicting 13Calpha chemical shifts for validation of protein structures. Journal of Biomolecular Nmr. 38: 221-35. PMID 17558470 DOI: 10.1007/S10858-007-9162-X |
0.427 |
|
| 2007 |
Vila JA, Ripoll DR, Scheraga HA. Use of 13Calpha chemical shifts in protein structure determination. The Journal of Physical Chemistry. B. 111: 6577-85. PMID 17516673 DOI: 10.1021/Jp0683871 |
0.424 |
|
| 2007 |
Welker E, Hathaway L, Xu G, Narayan M, Pradeep L, Shin HC, Scheraga HA. Oxidative folding and N-terminal cyclization of onconase. Biochemistry. 46: 5485-93. PMID 17439243 DOI: 10.1021/Bi602495A |
0.564 |
|
| 2007 |
Makowski M, Sobolewski E, Czaplewski C, Liwo A, OÅ‚dziej S, No JH, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains. The Journal of Physical Chemistry. B. 111: 2925-31. PMID 17388418 DOI: 10.1021/Jp065918C |
0.351 |
|
| 2007 |
Makowski M, Liwo A, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model. The Journal of Physical Chemistry. B. 111: 2910-6. PMID 17388416 DOI: 10.1021/Jp065916S |
0.322 |
|
| 2007 |
Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA. Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Research. 35: 2227-37. PMID 17369272 DOI: 10.1093/Nar/Gkm045 |
0.314 |
|
| 2007 |
Jagielska A, Scheraga HA. Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent. Journal of Computational Chemistry. 28: 1068-82. PMID 17279497 DOI: 10.1002/Jcc.20631 |
0.336 |
|
| 2007 |
Makowska J, Rodziewicz-Motowidlo S, Baginska K, Makowski M, Vila JA, Liwo A, Chmurzynski L, Scheraga HA. Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophysical Journal. 92: 2904-17. PMID 17277185 DOI: 10.1529/Biophysj.106.097550 |
0.389 |
|
| 2007 |
Rojas AV, Liwo A, Scheraga HA. Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. The Journal of Physical Chemistry. B. 111: 293-309. PMID 17201452 DOI: 10.1021/Jp065810X |
0.388 |
|
| 2007 |
Liwo A, Khalili M, Czaplewski C, Kalinowski S, OÅ‚dziej S, Wachucik K, Scheraga HA. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. The Journal of Physical Chemistry. B. 111: 260-85. PMID 17201450 DOI: 10.1021/Jp065380A |
0.392 |
|
| 2007 |
Villegas ME, Vila JA, Scheraga HA. Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. Journal of Biomolecular Nmr. 37: 137-46. PMID 17180547 DOI: 10.1007/S10858-006-9118-6 |
0.369 |
|
| 2007 |
Scheraga HA, Khalili M, Liwo A. Protein-folding dynamics: overview of molecular simulation techniques. Annual Review of Physical Chemistry. 58: 57-83. PMID 17034338 DOI: 10.1146/Annurev.Physchem.58.032806.104614 |
0.372 |
|
| 2007 |
KozÅowska U, Liwo A, Scheraga HA. Determination of virtual-bond-angle potentials of mean force for coarse-grained simulations of protein structure and folding from ab initio energy surfaces of terminally-blocked glycine, alanine, and proline Journal of Physics Condensed Matter. 19. DOI: 10.1088/0953-8984/19/28/285203 |
0.392 |
|
| 2007 |
Scheraga HA, Hao M. Entropy Sampling Monte Carlo for Polypeptides and Proteins Advances in Chemical Physics. 105: 243-272. DOI: 10.1002/9780470141649.Ch8 |
0.325 |
|
| 2006 |
Nanias M, Czaplewski C, Scheraga HA. Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. Journal of Chemical Theory and Computation. 2: 513-528. PMID 18797518 DOI: 10.1021/Ct050253O |
0.384 |
|
| 2006 |
Pradeep L, Shin HC, Scheraga HA. Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family. Febs Letters. 580: 5029-32. PMID 16949585 DOI: 10.1016/J.Febslet.2006.08.024 |
0.365 |
|
| 2006 |
Dyson HJ, Wright PE, Scheraga HA. The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 103: 13057-61. PMID 16916929 DOI: 10.1073/Pnas.0605504103 |
0.328 |
|
| 2006 |
Arnautova YA, Jagielska A, Scheraga HA. A new force field (ECEPP-05) for peptides, proteins, and organic molecules. The Journal of Physical Chemistry. B. 110: 5025-44. PMID 16526746 DOI: 10.1021/Jp054994X |
0.392 |
|
| 2006 |
Makowska J, Bagiñska K, Makowski M, Jagielska A, Liwo A, Kasprzykowski F, Chmurzyñski L, Scheraga HA. Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment. The Journal of Physical Chemistry. B. 110: 4451-8. PMID 16509748 DOI: 10.1021/Jp054814J |
0.348 |
|
| 2006 |
Makowska J, Rodziewicz-Motowidło S, Bagińska K, Vila JA, Liwo A, Chmurzyński L, Scheraga HA. Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 1744-9. PMID 16446433 DOI: 10.1073/Pnas.0510549103 |
0.408 |
|
| 2006 |
Xu G, Narayan M, Kurinov I, Ripoll DR, Welker E, Khalili M, Ealick SE, Scheraga HA. A localized specific interaction alters the unfolding pathways of structural homologues. Journal of the American Chemical Society. 128: 1204-13. PMID 16433537 DOI: 10.1021/Ja055313E |
0.607 |
|
| 2006 |
Zabrouskov V, Han X, Welker E, Zhai H, Lin C, van Wijk KJ, Scheraga HA, McLafferty FW. Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry. 45: 987-92. PMID 16411774 DOI: 10.1021/Bi0517584 |
0.309 |
|
| 2006 |
Khalili M, Liwo A, Scheraga HA. Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. Journal of Molecular Biology. 355: 536-47. PMID 16324712 DOI: 10.1016/J.Jmb.2005.10.056 |
0.409 |
|
| 2006 |
Chinchio M, Czaplewski C, Ołdziej S, Scheraga HA. A hierarchical multiscale approach to protein structure prediction: Production of low-resolution packing arrangements of helices and refinement of the best models with a united-residue force field Multiscale Modeling and Simulation. 5: 1175-1195. DOI: 10.1137/060649318 |
0.825 |
|
| 2006 |
Scheraga HA. THE EFFECT OF SOLUTES ON THE STRUCTURE OF WATER AND ITS IMPLICATIONS FOR PROTEIN STRUCTURE* Annals of the New York Academy of Sciences. 125: 253-276. DOI: 10.1111/J.1749-6632.1965.Tb45396.X |
0.32 |
|
| 2006 |
Scheraga HA, Liwo A, Oldziej S, Czaplewski C, Pillardy J, Lee J, Ripoll DR, Vila JA, Kazmierkiewicz R, Saunders JA, Arnautova YA, Gibson KD, Jagielska A, Khalili M, Chinchio M, et al. The Protein Folding Problem Lecture Notes in Computational Science and Engineering. 49: 90-100. |
0.785 |
|
| 2005 |
Khalili M, Liwo A, Jagielska A, Scheraga HA. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. The Journal of Physical Chemistry. B. 109: 13798-810. PMID 16852728 DOI: 10.1021/Jp058007W |
0.359 |
|
| 2005 |
Khalili M, Liwo A, Rakowski F, Grochowski P, Scheraga HA. Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. The Journal of Physical Chemistry. B. 109: 13785-97. PMID 16852727 DOI: 10.1021/Jp058008O |
0.315 |
|
| 2005 |
Czaplewski C, Liwo A, Ripoll DR, Scheraga HA. Molecular origin of anticooperativity in hydrophobic association. The Journal of Physical Chemistry. B. 109: 8108-19. PMID 16851948 DOI: 10.1021/Jp040691B |
0.316 |
|
| 2005 |
Day GM, Motherwell WD, Ammon HL, Boerrigter SX, Della Valle RG, Venuti E, Dzyabchenko A, Dunitz JD, Schweizer B, van Eijck BP, Erk P, Facelli JC, Bazterra VE, Ferraro MB, Hofmann DW, ... ... Scheraga HA, et al. A third blind test of crystal structure prediction. Acta Crystallographica. Section B, Structural Science. 61: 511-27. PMID 16186652 DOI: 10.1107/S0108768105016563 |
0.307 |
|
| 2005 |
Nanias M, Chinchio M, OÅ‚dziej S, Czaplewski C, Scheraga HA. Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. Journal of Computational Chemistry. 26: 1472-86. PMID 16088925 DOI: 10.1002/Jcc.20286 |
0.809 |
|
| 2005 |
Vila JA, Ripoll DR, Arnautova YA, Vorobjev YN, Scheraga HA. Coupling between conformation and proton binding in proteins. Proteins. 61: 56-68. PMID 16080152 DOI: 10.1002/Prot.20531 |
0.406 |
|
| 2005 |
Xu G, Narayan M, Scheraga HA. The oxidative folding rate of bovine pancreatic ribonuclease is enhanced by a covalently attached oligosaccharide. Biochemistry. 44: 9817-23. PMID 16008366 DOI: 10.1021/Bi0506932 |
0.515 |
|
| 2005 |
Ołdziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kaźmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, ... ... Scheraga HA, et al. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proceedings of the National Academy of Sciences of the United States of America. 102: 7547-52. PMID 15894609 DOI: 10.1073/Pnas.0502655102 |
0.81 |
|
| 2005 |
Ripoll DR, Vila JA, Scheraga HA. On the orientation of the backbone dipoles in native folds. Proceedings of the National Academy of Sciences of the United States of America. 102: 7559-64. PMID 15894608 DOI: 10.1073/Pnas.0502754102 |
0.391 |
|
| 2005 |
Cerovský V, Scheraga HA. Combined solid-phase/solution synthesis of large ribonuclease A C-terminal peptides containing a non-natural proline analog. The Journal of Peptide Research : Official Journal of the American Peptide Society. 65: 518-28. PMID 15885111 DOI: 10.1111/J.1399-3011.2005.00257.X |
0.302 |
|
| 2005 |
Leung HJ, Xu G, Narayan M, Scheraga HA. Impact of an easily reducible disulfide bond on the oxidative folding rate of multi-disulfide-containing proteins. The Journal of Peptide Research : Official Journal of the American Peptide Society. 65: 47-54. PMID 15686534 DOI: 10.1111/J.1399-3011.2004.00189.X |
0.574 |
|
| 2005 |
Liwo A, Khalili M, Scheraga HA. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America. 102: 2362-7. PMID 15677316 DOI: 10.1073/Pnas.0408885102 |
0.4 |
|
| 2005 |
Makowska J, Bagińska K, Kasprzykowski F, Vila JA, Jagielska A, Liwo A, Chmurzyński L, Scheraga HA. Interplay of charge distribution and conformation in peptides: comparison of theory and experiment. Biopolymers. 80: 214-24. PMID 15630705 DOI: 10.1002/Bip.20180 |
0.405 |
|
| 2004 |
Welker E, Maki K, Shastry MC, Juminaga D, Bhat R, Scheraga HA, Roder H. Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proceedings of the National Academy of Sciences of the United States of America. 101: 17681-6. PMID 15574490 DOI: 10.1073/Pnas.0407999101 |
0.556 |
|
| 2004 |
Gahl RF, Narayan M, Xu G, Scheraga HA. Trimethylamine-N-oxide modulates the reductive unfolding of onconase. Biochemical and Biophysical Research Communications. 325: 707-10. PMID 15541346 DOI: 10.1016/J.Bbrc.2004.10.088 |
0.558 |
|
| 2004 |
Vila JA, Baldoni HA, Scheraga HA. Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids. Protein Science : a Publication of the Protein Society. 13: 2939-48. PMID 15498939 DOI: 10.1110/Ps.04930804 |
0.343 |
|
| 2004 |
Dunitz JD, Scheraga HA. Exercises in prognostication: crystal structures and protein folding. Proceedings of the National Academy of Sciences of the United States of America. 101: 14309-11. PMID 15452353 DOI: 10.1073/Pnas.0405744101 |
0.367 |
|
| 2004 |
Khalili M, Saunders JA, Liwo A, OÅ‚dziej S, Scheraga HA. A united residue force-field for calcium-protein interactions. Protein Science : a Publication of the Protein Society. 13: 2725-35. PMID 15388862 DOI: 10.1110/Ps.04878904 |
0.352 |
|
| 2004 |
Scheraga HA, Liwo A, Oldziej S, Czaplewski C, Pillardy J, Ripoll DR, Vila JA, Kazmierkiewicz R, Saunders JA, Arnautova YA, Jagielska A, Chinchio M, Nanias M. The protein folding problem: global optimization of the force fields. Frontiers in Bioscience : a Journal and Virtual Library. 9: 3296-323. PMID 15353359 DOI: 10.2741/1482 |
0.813 |
|
| 2004 |
Vila JA, Baldoni HA, Ripoll DR, Scheraga HA. Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide. Proteins. 57: 87-98. PMID 15326595 DOI: 10.1002/Prot.20177 |
0.397 |
|
| 2004 |
Ripoll DR, Vila JA, Scheraga HA. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. Journal of Molecular Biology. 339: 915-25. PMID 15165859 DOI: 10.1016/J.Jmb.2004.04.002 |
0.425 |
|
| 2004 |
Xu G, Zhai H, Narayan M, McLafferty FW, Scheraga HA. Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry. Chemistry & Biology. 11: 517-24. PMID 15123246 DOI: 10.1016/J.Chembiol.2004.03.020 |
0.557 |
|
| 2004 |
Narayan M, Xu G, Ripoll DR, Zhai H, Breuker K, Wanjalla C, Leung HJ, Navon A, Welker E, McLafferty FW, Scheraga HA. Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. Journal of Molecular Biology. 338: 795-809. PMID 15099746 DOI: 10.1016/J.Jmb.2004.03.014 |
0.562 |
|
| 2004 |
Welker E, Hathaway L, Scheraga HA. A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins. Journal of the American Chemical Society. 126: 3720-1. PMID 15038718 DOI: 10.1021/Ja031658Q |
0.364 |
|
| 2004 |
Xu G, Narayan M, Welker E, Scheraga HA. Characterization of the fast-forming intermediate, des [30-75], in the reductive unfolding of onconase. Biochemistry. 43: 3246-54. PMID 15023075 DOI: 10.1021/Bi036215D |
0.57 |
|
| 2004 |
Dzyabchenko A, Scheraga HA. Model for the crystal packing and conformational changes of biphenyl in incommensurate phase transitions. Acta Crystallographica. Section B, Structural Science. 60: 228-37. PMID 15017097 DOI: 10.1107/S010876810400312X |
0.343 |
|
| 2004 |
Czaplewski C, Oldziej S, Liwo A, Scheraga HA. Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds. Protein Engineering, Design & Selection : Peds. 17: 29-36. PMID 14985535 DOI: 10.1093/Protein/Gzh003 |
0.418 |
|
| 2004 |
Vila JA, Baldoni HA, Ripoll DR, Ghosh A, Scheraga HA. Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophysical Journal. 86: 731-42. PMID 14747311 DOI: 10.1016/S0006-3495(04)74151-X |
0.391 |
|
| 2004 |
Kamikubo Y, Guzman RND, Kroon G, Curriden, Neels J, Dawson P, Oldziej S, Jagielska A, Scheraga HA, Loskutoff DJ, Dyson HJ. Structural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin B domain of human vitronectin Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr6160 |
0.304 |
|
| 2004 |
Oldziej S, Lagjewka J, Liwo A, Czaplewski C, Chinchio M, Nanias M, Scheraga HA. Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization Journal of Physical Chemistry B. 108: 16950-16959. DOI: 10.1021/Jp040329X |
0.772 |
|
| 2004 |
Oldziej S, Liwo A, Czaplewski C, Pillardy J, Scheraga HA. Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. off-lattice tests of the method with single proteins Journal of Physical Chemistry B. 108: 16934-16949. DOI: 10.1021/Jp0403285 |
0.328 |
|
| 2004 |
Liwo A, Artukowicz P, Oldziej S, Czaplewski C, Makowski M, Scheraga HA. Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 1. Tests of the approach using simple lattice protein models Journal of Physical Chemistry B. 108: 16918-16933. DOI: 10.1021/Jp040327C |
0.374 |
|
| 2004 |
Jagielska A, Arnautova YA, Scheraga HA. Derivation of a new force field for crystal-structure prediction using global optimization: Nonbonded potential parameters for amines, imidazoles, amides, and carboxylic acids Journal of Physical Chemistry B. 108: 12181-12196. DOI: 10.1021/Jp040115F |
0.314 |
|
| 2004 |
Liwo A, OÅdziej S, Czaplewski C, KozÅowska U, Scheraga HA. Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from Ab initio energy surfaces of model systems Journal of Physical Chemistry B. 108: 9421-9438. DOI: 10.1021/Jp030844F |
0.397 |
|
| 2004 |
Griffith JH, Scheraga HA. Statistical thermodynamics of aqueous solutions. I. Water structure, solutions with non-polar solutes, and hydrophobic interactions Journal of Molecular Structure: Theochem. 682: 97-113. DOI: 10.1016/J.Theochem.2004.06.003 |
0.332 |
|
| 2004 |
Czaplewski C, Liwo A, Pillardy J, OÅdziej S, Scheraga HA. Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation Polymer. 45: 677-686. DOI: 10.1016/J.Polymer.2003.10.081 |
0.391 |
|
| 2003 |
Narayan M, Xu G, Schultz SK, Scheraga HA. Assessing the magnitude of folding forces along the oxidative folding pathway of multi-disulfide-containing proteins. Journal of the American Chemical Society. 125: 16184-5. PMID 14692748 DOI: 10.1021/Ja0305398 |
0.607 |
|
| 2003 |
Vila JA, Ripoll DR, Scheraga HA. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proceedings of the National Academy of Sciences of the United States of America. 100: 14812-6. PMID 14638943 DOI: 10.1073/Pnas.2436463100 |
0.432 |
|
| 2003 |
Xu G, Narayan M, Welker E, Scheraga HA. A novel method to determine thermal transition curves of disulfide-containing proteins and their structured folding intermediates. Biochemical and Biophysical Research Communications. 311: 514-7. PMID 14592446 DOI: 10.1016/J.Bbrc.2003.10.039 |
0.562 |
|
| 2003 |
Shin HC, Narayan M, Song MC, Scheraga HA. Role of the [65-72] disulfide bond in oxidative folding of bovine pancreatic ribonuclease A. Biochemistry. 42: 11514-9. PMID 14516203 DOI: 10.1021/Bi030152H |
0.562 |
|
| 2003 |
LASKOWSKI M, WIDOM JM, MCFADDEN ML, SCHERAGA HA. Differential ultraviolet spectra of insulin. Biochimica Et Biophysica Acta. 19: 581-2. PMID 13315339 DOI: 10.1016/0006-3002(56)90502-9 |
0.574 |
|
| 2003 |
Narayan M, Welker E, Wanjalla C, Xu G, Scheraga HA. Shifting the competition between the intramolecular Reshuffling reaction and the direct oxidation reaction during the oxidative folding of kinetically trapped disulfide-insecure intermediates. Biochemistry. 42: 10783-9. PMID 12962503 DOI: 10.1021/Bi030141O |
0.541 |
|
| 2003 |
Narayan M, Welker E, Scheraga HA. Characterizing the unstructured intermediates in oxidative folding. Biochemistry. 42: 6947-55. PMID 12795589 DOI: 10.1021/Bi030054W |
0.59 |
|
| 2003 |
Vila JA, Baldoni HA, Ripoll DR, Scheraga HA. Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts. Journal of Biomolecular Nmr. 26: 113-30. PMID 12766407 DOI: 10.1023/A:1023524727484 |
0.378 |
|
| 2003 |
Bhat R, Wedemeyer WJ, Scheraga HA. Proline isomerization in bovine pancreatic ribonuclease A. 2. Folding conditions. Biochemistry. 42: 5722-8. PMID 12741829 DOI: 10.1021/bi030024t |
0.533 |
|
| 2003 |
Kaźmierkiewicz R, Liwo A, Scheraga HA. Addition of side chains to a known backbone with defined side-chain centroids. Biophysical Chemistry. 100: 261-80. PMID 12646370 DOI: 10.1016/S0301-4622(02)00285-5 |
0.387 |
|
| 2003 |
Saunders JA, Scheraga HA. Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC. Biopolymers. 68: 318-32. PMID 12601792 DOI: 10.1002/Bip.10227 |
0.414 |
|
| 2003 |
Saunders JA, Scheraga HA. Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search. Biopolymers. 68: 300-17. PMID 12601791 DOI: 10.1002/Bip.10226 |
0.402 |
|
| 2003 |
Narayan M, Welker E, Scheraga HA. Native conformational tendencies in unfolded polypeptides: development of a novel method to assess native conformational tendencies in the reduced forms of multiple disulfide-bonded proteins. Journal of the American Chemical Society. 125: 2036-7. PMID 12590517 DOI: 10.1021/Ja021252Y |
0.597 |
|
| 2003 |
Nanias M, Chinchio M, Pillardy J, Ripoll DR, Scheraga HA. Packing helices in proteins by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America. 100: 1706-10. PMID 12571353 DOI: 10.1073/Pnas.252760199 |
0.806 |
|
| 2003 |
Cerovský V, Welker E, Scheraga HA. A convenient incorporation of conformationally constrained 5,5-dimethylproline into the ribonuclease A 89-124 sequence by condensation of synthetic peptide fragments. The Journal of Peptide Research : Official Journal of the American Peptide Society. 61: 140-51. PMID 12558949 DOI: 10.1034/J.1399-3011.2003.00041.X |
0.335 |
|
| 2003 |
Fernández A, Scheraga HA. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 100: 113-8. PMID 12518060 DOI: 10.1073/Pnas.0136888100 |
0.372 |
|
| 2003 |
Fernández A, Scott LR, Scheraga HA. Amino Acid Residues at Protein-Protein Interfaces: Why Is Propensity so Different from Relative Abundance? Journal of Physical Chemistry B. 107: 9929-9932. DOI: 10.1021/Jp0348124 |
0.425 |
|
| 2003 |
Maksimiak K, Rodziewicz-Motowidlo S, Czaplewski C, Liwo A, Scheraga HA. Molecular simulation study of the potentials of mean force for the interactions between models of like-charged and between charged and nonpolar amino acid side chains in water Journal of Physical Chemistry B. 107: 13496-13504. DOI: 10.1021/Jp030691W |
0.312 |
|
| 2003 |
Arnautova YA, Jagielska A, Pillardy J, Scheraga HA. Derivation of a new force field for crystal-structure prediction using global optimization: Nonbonded potential parameters for hydrocarbons and alcohols Journal of Physical Chemistry B. 107: 7143-7154. DOI: 10.1021/Jp0301498 |
0.307 |
|
| 2003 |
Oldziej S, Kozlwska U, Liwo A, Scheraga HA. Determination of the potentials of mean force for rotation about Cα-Cα virtual bonds in polypeptides from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline Journal of Physical Chemistry A. 107: 8035-8046. DOI: 10.1021/Jp0223410 |
0.38 |
|
| 2003 |
Arnautova YA, Pillardy J, Czaplewski C, Scheraga HA. Global optimization-based method for deriving intermolecular potential parameters for crystals Journal of Physical Chemistry B. 107: 712-723. DOI: 10.1021/Jp0220433 |
0.328 |
|
| 2002 |
Vila JA, Ripoll DR, Baldoni HA, Scheraga HA. Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. Journal of Biomolecular Nmr. 24: 245-62. PMID 12522312 DOI: 10.1023/A:1021633403715 |
0.396 |
|
| 2002 |
Scheraga HA, Vila JA, Ripoll DR. Helix-coil transitions re-visited. Biophysical Chemistry. 101: 255-65. PMID 12488006 DOI: 10.1016/S0301-4622(02)00175-8 |
0.372 |
|
| 2002 |
Carty RP, Pincus MR, Scheraga HA. Interactions that favor the native over the non-native disulfide bond among residues 58-72 in the oxidative folding of bovine pancreatic ribonuclease A. Biochemistry. 41: 14815-9. PMID 12475229 DOI: 10.1021/Bi0205350 |
0.457 |
|
| 2002 |
Wedemeyer WJ, Welker E, Scheraga HA. Proline cis-trans isomerization and protein folding. Biochemistry. 41: 14637-44. PMID 12475212 DOI: 10.1021/Bi020574B |
0.375 |
|
| 2002 |
Navon A, Ittah V, Scheraga HA, Haas E. Formation of the hydrophobic core of ribonuclease A through sequential coordinated conformational transitions. Biochemistry. 41: 14225-31. PMID 12450386 DOI: 10.1021/Bi020506P |
0.406 |
|
| 2002 |
Motherwell WD, Ammon HL, Dunitz JD, Dzyabchenko A, Erk P, Gavezzotti A, Hofmann DW, Leusen FJ, Lommerse JP, Mooij WT, Price SL, Scheraga H, Schweizer B, Schmidt MU, van Eijck BP, et al. Crystal structure prediction of small organic molecules: a second blind test. Acta Crystallographica. Section B, Structural Science. 58: 647-61. PMID 12149555 DOI: 10.1107/S0108768102005669 |
0.301 |
|
| 2002 |
Ghosh A, Elber R, Scheraga HA. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proceedings of the National Academy of Sciences of the United States of America. 99: 10394-8. PMID 12140363 DOI: 10.1073/Pnas.142288099 |
0.391 |
|
| 2002 |
Shin HC, Song MC, Scheraga HA. Effect of protein disulfide isomerase on the rate-determining steps of the folding of bovine pancreatic ribonuclease A. Febs Letters. 521: 77-80. PMID 12067730 DOI: 10.1016/S0014-5793(02)02825-9 |
0.347 |
|
| 2002 |
English BP, Welker E, Narayan M, Scheraga HA. Development of a novel method to populate native disulfide-bonded intermediates for structural characterization of proteins: implications for the mechanism of oxidative folding of RNase A. Journal of the American Chemical Society. 124: 4995-9. PMID 11982363 DOI: 10.1021/Ja012634R |
0.768 |
|
| 2002 |
Kaźmierkiewicz R, Liwo A, Scheraga HA. Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. Journal of Computational Chemistry. 23: 715-23. PMID 11948589 DOI: 10.1002/Jcc.10068 |
0.394 |
|
| 2002 |
Scheraga HA, Pillardy J, Liwo A, Lee J, Czaplewski C, Ripoll DR, Wedemeyer WJ, Arnautova YA. Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. Journal of Computational Chemistry. 23: 28-34. PMID 11913387 DOI: 10.1002/Jcc.1154 |
0.422 |
|
| 2002 |
Low LK, Shin HC, Scheraga HA. Oxidative folding of bovine pancreatic ribonuclease A: insight into the overall catalysis of the refolding pathway by phosphate. Journal of Protein Chemistry. 21: 19-27. PMID 11902664 DOI: 10.1023/A:1014174930972 |
0.332 |
|
| 2002 |
Liwo A, Arłukowicz P, Czaplewski C, Ołdziej S, Pillardy J, Scheraga HA. A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proceedings of the National Academy of Sciences of the United States of America. 99: 1937-42. PMID 11854494 DOI: 10.1073/Pnas.032675399 |
0.39 |
|
| 2002 |
Wedemeyer WJ, Xu X, Welker E, Scheraga HA. Conformational propensities of protein folding intermediates: distribution of species in the 1S, 2S, and 3S ensembles of the [C40A,C95A] mutant of bovine pancreatic ribonuclease A. Biochemistry. 41: 1483-91. PMID 11814341 DOI: 10.1021/Bi011893Q |
0.406 |
|
| 2002 |
Czaplewski C, Ripoll DR, Liwo A, Rodziewicz-Motowid?o S, Wawak RJ, Scheraga HA. Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models? International Journal of Quantum Chemistry. 88: 41-55. DOI: 10.1002/Qua.10077 |
0.306 |
|
| 2001 |
Saito K, Welker E, Scheraga HA. Folding of a disulfide-bonded protein species with free thiol(s): competition between conformational folding and disulfide reshuffling in an intermediate of bovine pancreatic ribonuclease A. Biochemistry. 40: 15002-8. PMID 11732921 DOI: 10.1021/Bi010781W |
0.412 |
|
| 2001 |
Roisman LC, Piehler J, Trosset JY, Scheraga HA, Schreiber G. Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking. Proceedings of the National Academy of Sciences of the United States of America. 98: 13231-6. PMID 11698684 DOI: 10.1073/Pnas.221290398 |
0.324 |
|
| 2001 |
Pillardy J, Arnautova YA, Czaplewski C, Gibson KD, Scheraga HA. Conformation-family Monte Carlo: a new method for crystal structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 98: 12351-6. PMID 11606783 DOI: 10.1073/Pnas.231479298 |
0.338 |
|
| 2001 |
Scheraga HA, Wedemeyer WJ, Welker E. Bovine pancreatic ribonuclease A: oxidative and conformational folding studies. Methods in Enzymology. 341: 189-221. PMID 11582778 DOI: 10.1016/S0076-6879(01)41153-0 |
0.309 |
|
| 2001 |
Welker E, Wedemeyer WJ, Narayan M, Scheraga HA. Coupling of conformational folding and disulfide-bond reactions in oxidative folding of proteins. Biochemistry. 40: 9059-64. PMID 11478871 DOI: 10.1021/Bi010409G |
0.567 |
|
| 2001 |
Narayan M, Welker E, Scheraga HA. Development of a novel method to study the rate-determining step during protein regeneration: application to the oxidative folding of RNase A at low temperature reveals BPTI-like kinetic traps. Journal of the American Chemical Society. 123: 2909-10. PMID 11456989 DOI: 10.1021/Ja003934W |
0.516 |
|
| 2001 |
Cao A, Welker E, Scheraga HA. Effect of mutation of proline 93 on redox unfolding/folding of bovine pancreatic ribonuclease A. Biochemistry. 40: 8536-41. PMID 11456492 DOI: 10.1021/Bi010692J |
0.34 |
|
| 2001 |
Welker E, Wedemeyer WJ, Scheraga HA. A role for intermolecular disulfide bonds in prion diseases? Proceedings of the National Academy of Sciences of the United States of America. 98: 4334-6. PMID 11274354 DOI: 10.1073/Pnas.071066598 |
0.313 |
|
| 2001 |
Pillardy J, Czaplewski C, Liwo A, Lee J, Ripoll DR, Kaźmierkiewicz R, Oldziej S, Wedemeyer WJ, Gibson KD, Arnautova YA, Saunders J, Ye YJ, Scheraga HA. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America. 98: 2329-33. PMID 11226239 DOI: 10.1073/Pnas.041609598 |
0.384 |
|
| 2001 |
Welker E, Narayan M, Wedemeyer WJ, Scheraga HA. Structural determinants of oxidative folding in proteins. Proceedings of the National Academy of Sciences of the United States of America. 98: 2312-6. PMID 11226236 DOI: 10.1073/Pnas.041615798 |
0.545 |
|
| 2001 |
Vila JA, Ripoll DR, Scheraga HA. Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers. 58: 235-46. PMID 11169384 DOI: 10.1002/1097-0282(200103)58:3<235::Aid-Bip1001>3.0.Co;2-T |
0.422 |
|
| 2001 |
Navon A, Ittah V, Landsman P, Scheraga HA, Haas E. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry. 40: 105-18. PMID 11141061 DOI: 10.1021/Bi001946O |
0.414 |
|
| 2001 |
Navon A, Ittah V, Laity JH, Scheraga HA, Haas E, Gussakovsky EE. Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A. Biochemistry. 40: 93-104. PMID 11141060 DOI: 10.1021/Bi001945W |
0.353 |
|
| 2001 |
Liwo A, Czaplewski C, Pillardy J, Scheraga HA. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field The Journal of Chemical Physics. 115: 2323-2347. DOI: 10.1063/1.1383989 |
0.382 |
|
| 2001 |
Lee J, Ripoll DR, Czaplewski C, Pillardy J, Wedemeyer WJ, Scheraga HA. Optimization of parameters in macromolecular potential energy functions by conformational space annealing Journal of Physical Chemistry B. 105: 7291-7298. DOI: 10.1021/Jp011102U |
0.343 |
|
| 2001 |
Pillardy J, Czaplewski C, Liwo A, Wedemeyer WJ, Lee J, Ripoll DR, Arłukowicz P, Ołdziej S, Arnautova YA, Scheraga HA. Development of physics-based energy functions that predict medium-resolution structures for proteins of the α, β, and α/β structural classes Journal of Physical Chemistry B. 105: 7299-7311. DOI: 10.1021/Jp0111012 |
0.3 |
|
| 2001 |
Narayan M, Welker E, Wedemeyer WJ, Scheraga HA. ChemInform Abstract: Oxidative Folding of Proteins Cheminform. 32: no-no. DOI: 10.1002/chin.200106255 |
0.46 |
|
| 2000 |
DONOVAN JW, LASKOWSKI M, SCHERAGA HA. Influenza of ionization of carboxyl groups on the ultraviolet absorption spectrum of lysozyme. Biochimica Et Biophysica Acta. 29: 455-6. PMID 13572380 DOI: 10.1016/0006-3002(58)90221-X |
0.575 |
|
| 2000 |
Narayan M, Welker E, Wedemeyer WJ, Scheraga HA. Oxidative folding of proteins. Accounts of Chemical Research. 33: 805-12. PMID 11087317 DOI: 10.1021/Ar000063M |
0.532 |
|
| 2000 |
Vila JA, Ripoll DR, Scheraga HA. Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proceedings of the National Academy of Sciences of the United States of America. 97: 13075-9. PMID 11078529 DOI: 10.1073/Pnas.240455797 |
0.419 |
|
| 2000 |
Czaplewski C, Rodziewicz-Motowidło S, Liwo A, Ripoll DR, Wawak RJ, Scheraga HA. Molecular simulation study of cooperativity in hydrophobic association. Protein Science : a Publication of the Protein Society. 9: 1235-45. PMID 10892816 DOI: 10.1110/Ps.9.6.1235 |
0.322 |
|
| 2000 |
Shin HC, Scheraga HA. Catalysis of the oxidative folding of bovine pancreatic ribonuclease A by protein disulfide isomerase. Journal of Molecular Biology. 300: 995-1003. PMID 10891284 DOI: 10.1006/Jmbi.2000.3928 |
0.357 |
|
| 2000 |
Wedemeyer WJ, Welker E, Narayan M, Scheraga HA. Disulfide bonds and protein folding Biochemistry. 39: 7032. PMID 10841785 |
0.519 |
|
| 2000 |
Low LK, Shin HC, Narayan M, Wedemeyer WJ, Scheraga HA. Acceleration of oxidative folding of bovine pancreatic ribonuclease A by anion-induced stabilization and formation of structured native-like intermediates. Febs Letters. 472: 67-72. PMID 10781807 DOI: 10.1016/S0014-5793(00)01432-0 |
0.56 |
|
| 2000 |
Song MC, Scheraga HA. Formation of native structure by intermolecular thiol-disulfide exchange reactions without oxidants in the folding of bovine pancreatic ribonuclease A. Febs Letters. 471: 177-81. PMID 10767418 DOI: 10.1016/S0014-5793(00)01386-7 |
0.358 |
|
| 2000 |
Wedemeyer WJ, Welker E, Narayan M, Scheraga HA. Disulfide bonds and protein folding. Biochemistry. 39: 4207-16. PMID 10757967 DOI: 10.1021/Bi992922O |
0.61 |
|
| 2000 |
Xiong Y, Juminaga D, Swapna GV, Wedemeyer WJ, Scheraga HA, Montelione GT. Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A. Protein Science : a Publication of the Protein Society. 9: 421-6. PMID 10716195 DOI: 10.1110/Ps.9.2.421 |
0.541 |
|
| 2000 |
Shimotakahara S, Rios C, Laity J, Zimmerman D, Scheraga H, Montelione G. 1H, 13C and 15N Resonance Assignments for the Bovine Pancreatic [C65S, C72S] Ribonuclease A at pH* 4.6 and Temperature of 20 deg. C Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr4031 |
0.754 |
|
| 2000 |
Pillardy J, Wawak RJ, Arnautova YA, Czaplewski C, Scheraga HA. Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions† Journal of the American Chemical Society. 122: 907-921. DOI: 10.1021/Ja9929990 |
0.343 |
|
| 2000 |
Lee J, Liwo A, Ripoll DR, Pillardy J, Saunders JA, Gibson KD, Scheraga HA. Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets International Journal of Quantum Chemistry. 77: 90-117. DOI: 10.1002/(Sici)1097-461X(2000)77:1<90::Aid-Qua10>3.0.Co;2-L |
0.456 |
|
| 1999 |
No KT, Kim SG, Cho KH, Scheraga HA. Description of hydration free energy density as a function of molecular physical properties. Biophysical Chemistry. 78: 127-45. PMID 17030307 DOI: 10.1016/S0301-4622(98)00225-7 |
0.499 |
|
| 1999 |
Laity JH, Montelione GT, Scheraga HA. Comparison of local and global stability of an analogue of a disulfide-folding intermediate with those of the wild-type protein in bovine pancreatic ribonuclease A: identification of specific regions of stable structure along the oxidative folding pathway. Biochemistry. 38: 16432-42. PMID 10600104 DOI: 10.1021/Bi9911684 |
0.531 |
|
| 1999 |
Welker E, Narayan M, Volles MJ, Scheraga HA. Two new structured intermediates in the oxidative folding of RNase A. Febs Letters. 460: 477-9. PMID 10556520 DOI: 10.1016/S0014-5793(99)01391-5 |
0.544 |
|
| 1999 |
Lee J, Liwo A, Ripoll DR, Pillardy J, Scheraga HA. Calculation of protein conformation by global optimization of a potential energy function. Proteins. 204-8. PMID 10526370 DOI: 10.1002/(Sici)1097-0134(1999)37:3+<204::Aid-Prot26>3.0.Co;2-F |
0.425 |
|
| 1999 |
Ripoll DR, Vila JA, Villegas ME, Scheraga HA. On the pH-conformational dependence of the unblocked SYPYD peptide. Journal of Molecular Biology. 292: 431-40. PMID 10493886 DOI: 10.1006/Jmbi.1999.3082 |
0.357 |
|
| 1999 |
Shin HC, Scheraga HA. Effect of protein disulfide isomerase on the regeneration of bovine ribonuclease A with dithiothreitol. Febs Letters. 456: 143-5. PMID 10452546 DOI: 10.1016/S0014-5793(99)00946-1 |
0.325 |
|
| 1999 |
Volles MJ, Xu X, Scheraga HA. Distribution of disulfide bonds in the two-disulfide intermediates in the regeneration of bovine pancreatic ribonuclease A: further insights into the folding process. Biochemistry. 38: 7284-93. PMID 10353840 DOI: 10.1021/Bi990570F |
0.393 |
|
| 1999 |
Maurer MC, Trosset JY, Lester CC, DiBella EE, Scheraga HA. New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program. Proteins. 34: 29-48. PMID 10336381 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<29::Aid-Prot4>3.0.Co;2-U |
0.383 |
|
| 1999 |
Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA. Protein structure prediction by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America. 96: 5482-5. PMID 10318909 DOI: 10.1073/Pnas.96.10.5482 |
0.403 |
|
| 1999 |
Iwaoka M, Wedemeyer WJ, Scheraga HA. Conformational unfolding studies of three-disulfide mutants of bovine pancreatic ribonuclease A and the coupling of proline isomerization to disulfide redox reactions. Biochemistry. 38: 2805-15. PMID 10052952 DOI: 10.1021/Bi982593K |
0.383 |
|
| 1999 |
Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proceedings of the National Academy of Sciences of the United States of America. 96: 2025-30. PMID 10051588 DOI: 10.1073/Pnas.96.5.2025 |
0.42 |
|
| 1999 |
Welker E, Scheraga HA. Use of benzyl mercaptan for direct preparation of long polypeptide benzylthio esters as substrates of subtiligase. Biochemical and Biophysical Research Communications. 254: 147-51. PMID 9920748 DOI: 10.1006/Bbrc.1998.9913 |
0.308 |
|
| 1999 |
Scheraga HA, Lee J, Pillardy J, Ye Y, Liwo A, Ripoll D. Journal of Global Optimization. 15: 235-260. DOI: 10.1023/A:1008328218931 |
0.349 |
|
| 1999 |
Locardi E, Kwak J, Scheraga HA, Goodman M. Thermodynamics of formation of the triple helix from free chains and from template-constrained chains of collagen-like monodisperse poly(gly-pro-hyp) structures Journal of Physical Chemistry A. 103: 10561-10566. DOI: 10.1021/Jp9925435 |
0.343 |
|
| 1999 |
Pillardy J, Liwo A, Groth M, Scheraga HA. An Efficient Deformation-Based Global Optimization Method for Off-Lattice Polymer Chains: Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM). Application to United-Residue Polypeptide Chains The Journal of Physical Chemistry B. 103: 7353-7366. DOI: 10.1021/Jp991014Y |
0.326 |
|
| 1999 |
An SSA, Lester CC, Peng JL, Li YJ, Rothwarf DM, Welker E, Thannhauser TW, Zhang LS, Tam JP, Scheraga HA. Retention of the cis proline conformation in tripeptide fragments of bovine pancreatic ribonuclease A containing a non-natural proline analogue, 5,5-dimethylproline Journal of the American Chemical Society. 121: 11558-11566. DOI: 10.1021/Ja9930317 |
0.362 |
|
| 1999 |
Ye Y, Ripoll D, Scheraga H. Kinetics of cooperative protein folding involving two separate conformational families Computational and Theoretical Polymer Science. 9: 359-370. DOI: 10.1016/S1089-3156(99)00031-8 |
0.422 |
|
| 1999 |
Liwo A, Pillardy J, Kaźmierkiewicz R, Wawak RJ, Groth M, Czaplewski C, Ołdziej S, Scheraga HA. Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods Theoretical Chemistry Accounts. 101: 16-20. DOI: 10.1007/S002140050399 |
0.428 |
|
| 1999 |
Lee J, Scheraga HA. Conformational space annealing by parallel computations: Extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin International Journal of Quantum Chemistry. 75: 255-265. DOI: 10.1002/(Sici)1097-461X(1999)75:3<255::Aid-Qua15>3.0.Co;2-V |
0.398 |
|
| 1999 |
Wedemeyer WJ, Scheraga HA. Exact analytical loop closure in proteins using polynomial equations Journal of Computational Chemistry. 20: 819-844. DOI: 10.1002/(Sici)1096-987X(199906)20:8<819::Aid-Jcc8>3.0.Co;2-Y |
0.317 |
|
| 1999 |
Trosset J, Scheraga HA. Prodock: Software package for protein modeling and docking Journal of Computational Chemistry. 20: 412-427. DOI: 10.1002/(Sici)1096-987X(199903)20:4<412::Aid-Jcc3>3.0.Co;2-N |
0.397 |
|
| 1998 |
SCHERAGA HA. Helix-random coil transformations in deuterated macromolecules. Annals of the New York Academy of Sciences. 84: 608-16. PMID 13747498 DOI: 10.1111/J.1749-6632.1960.Tb39094.X |
0.301 |
|
| 1998 |
Scheraga HA. Theory of hydrophobic interactions. Journal of Biomolecular Structure & Dynamics. 16: 447-60. PMID 9833681 DOI: 10.1080/07391102.1998.10508260 |
0.319 |
|
| 1998 |
Vila JA, Ripoll DR, Villegas ME, Vorobjev YN, Scheraga HA. Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices. Biophysical Journal. 75: 2637-46. PMID 9826588 DOI: 10.1016/S0006-3495(98)77709-4 |
0.433 |
|
| 1998 |
Ripoll DR, Liwo A, Scheraga HA. New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin. Biopolymers. 46: 117-26. PMID 9664845 DOI: 10.1002/(Sici)1097-0282(199808)46:2<117::Aid-Bip6>3.0.Co;2-P |
0.412 |
|
| 1998 |
Lee J, Scheraga HA, Rackovsky S. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers. 46: 103-16. PMID 9664844 DOI: 10.1002/(Sici)1097-0282(199808)46:2<103::Aid-Bip5>3.0.Co;2-Q |
0.785 |
|
| 1998 |
Trosset JY, Scheraga HA. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. Proceedings of the National Academy of Sciences of the United States of America. 95: 8011-5. PMID 9653131 DOI: 10.1073/Pnas.95.14.8011 |
0.339 |
|
| 1998 |
Pearson MA, Karplus PA, Dodge RW, Laity JH, Scheraga HA. Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A. Protein Science : a Publication of the Protein Society. 7: 1255-8. PMID 9605332 DOI: 10.1002/Pro.5560070522 |
0.404 |
|
| 1998 |
DiBella EE, Scheraga HA. Thrombin specificity: further evidence for the importance of the beta-insertion loop and Trp96. Implications of the hydrophobic interaction between Trp96 and Pro60B Pro60C for the activity of thrombin. Journal of Protein Chemistry. 17: 197-208. PMID 9588943 DOI: 10.1023/A:1022524416221 |
0.321 |
|
| 1998 |
Xu X, Scheraga HA. Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40-95] disulfide bond. Biochemistry. 37: 7561-71. PMID 9585571 DOI: 10.1021/Bi980086X |
0.342 |
|
| 1998 |
Maurer MC, Peng JL, An SS, Trosset JY, Henschen-Edman A, Scheraga HA. Structural examination of the influence of phosphorylation on the binding of fibrinopeptide A to bovine thrombin. Biochemistry. 37: 5888-902. PMID 9558322 DOI: 10.1021/Bi972538W |
0.355 |
|
| 1998 |
Hao MH, Scheraga HA. Molecular mechanisms for cooperative folding of proteins. Journal of Molecular Biology. 277: 973-83. PMID 9545385 DOI: 10.1006/Jmbi.1998.1658 |
0.423 |
|
| 1998 |
Houry WA, Sauder JM, Roder H, Scheraga HA. Definition of amide protection factors for early kinetic intermediates in protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 4299-302. PMID 9539731 DOI: 10.1073/pnas.95.8.4299 |
0.613 |
|
| 1998 |
Iwaoka M, Juminaga D, Scheraga HA. Regeneration of three-disulfide mutants of bovine pancreatic ribonuclease A missing the 65-72 disulfide bond: characterization of a minor folding pathway of ribonuclease A and kinetic roles of Cys65 and Cys72. Biochemistry. 37: 4490-501. PMID 9521769 DOI: 10.1021/Bi9725327 |
0.334 |
|
| 1998 |
Rothwarf DM, Li YJ, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A: detailed kinetic analysis of two independent folding pathways. Biochemistry. 37: 3767-76. PMID 9521696 DOI: 10.1021/Bi972823F |
0.322 |
|
| 1998 |
Rothwarf DM, Li YJ, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A: identification of two nativelike three-disulfide intermediates involved in separate pathways. Biochemistry. 37: 3760-6. PMID 9521695 DOI: 10.1021/Bi972822N |
0.324 |
|
| 1998 |
Thannhauser TW, Sherwood RW, Scheraga HA. Determination of the cysteine and cystine content of proteins by amino acid analysis: application to the characterization of disulfide-coupled folding intermediates. Journal of Protein Chemistry. 17: 37-43. PMID 9491926 DOI: 10.1023/A:1022586413862 |
0.348 |
|
| 1998 |
He S, Scheraga HA. Brownian dynamics simulations of protein folding The Journal of Chemical Physics. 108: 287-300. DOI: 10.1063/1.475379 |
0.379 |
|
| 1998 |
He S, Scheraga HA. Macromolecular conformational dynamics in torsional angle space The Journal of Chemical Physics. 108: 271-286. DOI: 10.1063/1.475378 |
0.317 |
|
| 1998 |
Vila JA, Ripoll DR, Vorobjev YN, Scheraga HA. Computation of the Structure-Dependent pKaShifts in a Polypentapeptide of the Poly[fv(IPGVG),fE(IPGEG)] Family The Journal of Physical Chemistry B. 102: 3065-3067. DOI: 10.1021/Jp980563L |
0.334 |
|
| 1998 |
Li Y, Rothwarf DM, Scheraga HA. An Unusual Adduct of Dithiothreitol with a Pair of Cysteine Residues of a Protein as a Stable Folding Intermediate Journal of the American Chemical Society. 120: 2668-2669. DOI: 10.1021/Ja973625E |
0.403 |
|
| 1998 |
Hao M, Scheraga HA. Theory of Two-State Cooperative Folding of Proteins Accounts of Chemical Research. 31: 433-440. DOI: 10.1021/Ar960288Q |
0.321 |
|
| 1998 |
Rothwarf DM, Davenport VG, Shi P, Peng J, Scheraga HA. Use of sequence-specific tri-block copolymers to determine the helix-forming tendencies of amino acids Biopolymers. 39: 531-536. DOI: 10.1002/(Sici)1097-0282(199610)39:4<531::Aid-Bip5>3.0.Co;2-Y |
0.31 |
|
| 1998 |
Liwo A, Ka?mierkiewicz R, Czaplewski C, Groth M, O?dziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials Journal of Computational Chemistry. 19: 259-276. DOI: 10.1002/(Sici)1096-987X(199802)19:3<259::Aid-Jcc1>3.0.Co;2-S |
0.388 |
|
| 1998 |
Oberlin D, Scheraga HA. B-spline method for energy minimization in grid-based molecular mechanics calculations Journal of Computational Chemistry. 19: 71-85. DOI: 10.1002/(Sici)1096-987X(19980115)19:1<71::Aid-Jcc6>3.0.Co;2-W |
0.321 |
|
| 1997 |
Lester CC, Xu X, Laity JH, Shimotakahara S, Scheraga HA. Regeneration studies of an analog of ribonuclease A missing disulfide bonds 65-72 and 40-95. Biochemistry. 36: 13068-76. PMID 9335569 DOI: 10.1021/Bi970954A |
0.386 |
|
| 1997 |
Laity JH, Lester CC, Shimotakahara S, Zimmerman DE, Montelione GT, Scheraga HA. Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A. Biochemistry. 36: 12683-99. PMID 9335525 DOI: 10.1021/Bi970878B |
0.506 |
|
| 1997 |
Shimotakahara S, Rios CB, Laity JH, Zimmerman DE, Scheraga HA, Montelione GT. NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms. Biochemistry. 36: 6915-29. PMID 9188686 DOI: 10.1021/Bi963024K |
0.511 |
|
| 1997 |
Thannhauser TW, Rothwarf DM, Scheraga HA. Kinetic studies of the regeneration of recombinant hirudin variant 1 with oxidized and reduced dithiothreitol. Biochemistry. 36: 2154-65. PMID 9047315 DOI: 10.1021/Bi962340W |
0.313 |
|
| 1997 |
Ashkenazi G, Ripoll DR, Lotan N, Scheraga HA. A molecular switch for biochemical logic gates: conformational studies. Biosensors & Bioelectronics. 12: 85-95. PMID 9011022 DOI: 10.1016/S0956-5663(97)87054-6 |
0.364 |
|
| 1997 |
Hao M, Scheraga HA. Characterization of foldable protein models: Thermodynamics, folding kinetics and force field The Journal of Chemical Physics. 107: 8089-8102. DOI: 10.1063/1.475072 |
0.382 |
|
| 1997 |
Hao M, Scheraga HA. On foldable protein-like models; a statistical-mechanical study with Monte Carlo simulations Physica a: Statistical Mechanics and Its Applications. 244: 124-146. DOI: 10.1016/S0378-4371(97)00222-7 |
0.359 |
|
| 1997 |
Collet O, Prémilat S, Maigret B, Scheraga HA. Comparison of explicit and implicit treatments of solvation: Application to angiotensin II Biopolymers. 42: 363-371. DOI: 10.1002/(Sici)1097-0282(199709)42:3<363::Aid-Bip8>3.0.Co;2-K |
0.341 |
|
| 1997 |
Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: Conformational space annealing Journal of Computational Chemistry. 18: 1222-1232. DOI: 10.1002/(Sici)1096-987X(19970715)18:9<1222::Aid-Jcc10>3.0.Co;2-7 |
0.374 |
|
| 1997 |
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, O?dziej S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization Journal of Computational Chemistry. 18: 874-887. DOI: 10.1002/(Sici)1096-987X(199705)18:7<874::Aid-Jcc2>3.0.Co;2-O |
0.344 |
|
| 1997 |
Liwo A, O?dziej S, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data Journal of Computational Chemistry. 18: 849-873. DOI: 10.1002/(Sici)1096-987X(199705)18:7<849::Aid-Jcc1>3.0.Co;2-R |
0.418 |
|
| 1997 |
Vorobjev YN, Scheraga HA. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent Journal of Computational Chemistry. 18: 569-583. DOI: 10.1002/(Sici)1096-987X(199703)18:4<569::Aid-Jcc10>3.0.Co;2-B |
0.329 |
|
| 1997 |
Gibson KD, Scheraga HA. Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops Journal of Computational Chemistry. 18: 403-415. DOI: 10.1002/(Sici)1096-987X(199702)18:3<403::Aid-Jcc10>3.0.Co;2-J |
0.333 |
|
| 1996 |
Lee J, Scheraga HA, Rackovsky S. Computational study of packing a collagen-like molecule: quasi-hexagonal vs "Smith" collagen microfibril model. Biopolymers. 40: 595-607. PMID 9140199 DOI: 10.1002/(Sici)1097-0282(1996)40:6<595::Aid-Bip1>3.0.Co;2-R |
0.764 |
|
| 1996 |
Ripoll DR, Vorobjev YN, Liwo A, Vila JA, Scheraga HA. Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. Journal of Molecular Biology. 264: 770-83. PMID 8980685 DOI: 10.1006/Jmbi.1996.0676 |
0.406 |
|
| 1996 |
Rothwarf DM, Scheraga HA. Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme. Biochemistry. 35: 13797-807. PMID 8901522 DOI: 10.1021/Bi9608119 |
0.366 |
|
| 1996 |
Rabow AA, Scheraga HA. Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator. Protein Science : a Publication of the Protein Society. 5: 1800-15. PMID 8880904 DOI: 10.1002/Pro.5560050906 |
0.311 |
|
| 1996 |
Sendak RA, Rothwarf DM, Wedemeyer WJ, Houry WA, Scheraga HA. Kinetic and thermodynamic studies of the folding/unfolding of a tryptophan-containing mutant of ribonuclease A. Biochemistry. 35: 12978-92. PMID 8841145 DOI: 10.1021/Bi961280R |
0.644 |
|
| 1996 |
Kombo DC, Némethy G, Gibson KD, Ross JB, Rackovsky S, Scheraga HA. Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor. Journal of Protein Chemistry. 15: 77-86. PMID 8838592 DOI: 10.1007/Bf01886813 |
0.798 |
|
| 1996 |
Houry WA, Scheraga HA. Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange. Biochemistry. 35: 11734-46. PMID 8794754 DOI: 10.1021/Bi961085C |
0.681 |
|
| 1996 |
Houry WA, Scheraga HA. Nature of the unfolded state of ribonuclease A: effect of cis-trans X-Pro peptide bond isomerization. Biochemistry. 35: 11719-33. PMID 8794753 DOI: 10.1021/Bi960745A |
0.616 |
|
| 1996 |
Houry WA, Rothwarf DM, Scheraga HA. Circular dichroism evidence for the presence of burst-phase intermediates on the conformational folding pathway of ribonuclease A. Biochemistry. 35: 10125-33. PMID 8756476 DOI: 10.1021/Bi960617M |
0.629 |
|
| 1996 |
Scheraga HA. Recent developments in the theory of protein folding: searching for the global energy minimum. Biophysical Chemistry. 59: 329-39. PMID 8672720 DOI: 10.1016/0301-4622(95)00126-3 |
0.375 |
|
| 1996 |
Hao MH, Scheraga HA. How optimization of potential functions affects protein folding. Proceedings of the National Academy of Sciences of the United States of America. 93: 4984-9. PMID 8643516 DOI: 10.1073/Pnas.93.10.4984 |
0.352 |
|
| 1996 |
Xu X, Rothwarf DM, Scheraga HA. Nonrandom distribution of the one-disulfide intermediates in the regeneration of ribonuclease A. Biochemistry. 35: 6406-17. PMID 8639587 DOI: 10.1021/Bi960090D |
0.327 |
|
| 1996 |
Dodge RW, Scheraga HA. Folding and unfolding kinetics of the proline-to-alanine mutants of bovine pancreatic ribonuclease A. Biochemistry. 35: 1548-59. PMID 8634286 DOI: 10.1021/Bi952348Q |
0.377 |
|
| 1996 |
Kombo DC, Némethy G, Gibson KD, Rackovsky S, Scheraga HA. Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor. Journal of Molecular Biology. 256: 517-32. PMID 8604135 DOI: 10.1006/Jmbi.1996.0105 |
0.788 |
|
| 1996 |
Kang YK, No KT, Scheraga HA. Intrinsic Torsional Potential Parameters for Conformational Analysis of Peptides and Proteins The Journal of Physical Chemistry. 100: 15588-15598. DOI: 10.1021/Jp9611434 |
0.41 |
|
| 1996 |
Hao M, Scheraga HA. Optimizing Potential Functions for Protein Folding The Journal of Physical Chemistry. 100: 14540-14548. DOI: 10.1021/Jp960856J |
0.378 |
|
| 1996 |
Augspurger JD, Scheraga HA. An efficient, differentiable hydration potential for peptides and proteins Journal of Computational Chemistry. 17: 1549-1558. DOI: 10.1002/(Sici)1096-987X(199610)17:13<1549::Aid-Jcc6>3.0.Co;2-S |
0.302 |
|
| 1996 |
Cheng B, Nayeem A, Scheraga HA. From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins Journal of Computational Chemistry. 17: 1453-1480. DOI: 10.1002/(Sici)1096-987X(199609)17:12<1453::Aid-Jcc6>3.0.Co;2-J |
0.381 |
|
| 1995 |
Joseph MP, Maigret B, Scheraga HA. Proposals for the angiotensin II receptor-bound conformation by comparative computer modeling of AII and cyclic analogs. International Journal of Peptide and Protein Research. 46: 514-26. PMID 8748712 DOI: 10.1111/J.1399-3011.1995.Tb01607.X |
0.379 |
|
| 1995 |
Lester CC, Wang B, Wu R, Scheraga HA. Structure-function studies of mEGF: probing the type I beta-turn between residues 25 and 26. Journal of Protein Chemistry. 14: 753-62. PMID 8747437 DOI: 10.1007/Bf01886915 |
0.351 |
|
| 1995 |
Buckler DR, Haas E, Scheraga HA. Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved noradiative dynamic excitation energy transfer between site-specific extrinsic probes. Biochemistry. 34: 15965-78. PMID 8519753 DOI: 10.1021/Bi00049A011 |
0.352 |
|
| 1995 |
Vitagliano L, Némethy G, Zagari A, Scheraga HA. Structure of the type I collagen molecule based on conformational energy computations: the triple-stranded helix and the N-terminal telopeptide. Journal of Molecular Biology. 247: 69-80. PMID 7897661 DOI: 10.1006/Jmbi.1994.0123 |
0.432 |
|
| 1995 |
DiBella EE, Maurer MC, Scheraga HA. Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin. The Journal of Biological Chemistry. 270: 163-9. PMID 7814368 DOI: 10.1074/Jbc.270.1.163 |
0.328 |
|
| 1995 |
Paterlini MG, Némethy G, Scheraga HA. The energy of formation of internal loops in triple-helical collagen polypeptides. Biopolymers. 35: 607-19. PMID 7766826 DOI: 10.1002/bip.360350607 |
0.329 |
|
| 1995 |
Ashton RW, Scheraga HA. Preparation and characterization of anhydrothrombin. Biochemistry. 34: 6454-63. PMID 7756277 DOI: 10.1021/Bi00019A027 |
0.319 |
|
| 1995 |
Houry WA, Rothwarf DM, Scheraga HA. The nature of the initial step in the conformational folding of disulphide-intact ribonuclease A. Nature Structural Biology. 2: 495-503. PMID 7664113 DOI: 10.1038/Nsb0695-495 |
0.645 |
|
| 1995 |
Li YJ, Rothwarf DM, Scheraga HA. Mechanism of reductive protein unfolding. Nature Structural Biology. 2: 489-94. PMID 7664112 DOI: 10.1038/Nsb0695-489 |
0.368 |
|
| 1995 |
Ni F, Zhu Y, Scheraga HA. Thrombin-bound structures of designed analogs of human fibrinopeptide A determined by quantitative transferred NOE spectroscopy: a new structural basis for thrombin specificity. Journal of Molecular Biology. 252: 656-71. PMID 7563081 DOI: 10.1006/Jmbi.1995.0527 |
0.421 |
|
| 1995 |
Hao M, Scheraga HA. Statistical thermodynamics of protein folding: Comparison of a mean‐field theory with Monte Carlo simulations The Journal of Chemical Physics. 102: 1334-1348. DOI: 10.1063/1.468920 |
0.414 |
|
| 1995 |
Vorobjev YN, Scheraga HA, Honig B. Theoretical Modeling of Electrostatic Effects of Titratable Side Chain Groups on Protein Conformation in a Polar Ionic Solution. 2. pH-Induced Helix-Coil Transition of Poly(L-lysine) in Water and Methanol Ionic Solutions The Journal of Physical Chemistry. 99: 7180-7187. DOI: 10.1021/J100018A060 |
0.346 |
|
| 1995 |
No KT, Kwon OY, Kim SY, Jhon MS, Scheraga HA. A Simple Functional Representation of Angular-Dependent Hydrogen-Bonded Systems. 1. Amide, Carboxylic Acid, and Amide-Carboxylic Acid Pairs The Journal of Physical Chemistry. 99: 3478-3486. DOI: 10.1021/J100011A013 |
0.306 |
|
| 1995 |
Ripoll DR, Pottle MS, Gibson KD, Scheraga HA, Liwo A. Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer Journal of Computational Chemistry. 16: 1153-1163. DOI: 10.1002/Jcc.540160909 |
0.32 |
|
| 1994 |
Houry WA, Rothwarf DM, Scheraga HA. A very fast phase in the refolding of disulfide-intact ribonuclease A: implications for the refolding and unfolding pathways. Biochemistry. 33: 2516-30. PMID 8117713 DOI: 10.1021/Bi00175A022 |
0.64 |
|
| 1994 |
Zagari A, Palmer KA, Gibson KD, Némethy G, Scheraga HA. The effect of the l-azetidine-2-carboxylic acid residue on protein conformation. IV. Local substitutions in the collagen triple helix. Biopolymers. 34: 51-60. PMID 8110968 DOI: 10.1002/Bip.360340107 |
0.407 |
|
| 1994 |
Talluri S, Rothwarf DM, Scheraga HA. Structural characterization of a three-disulfide intermediate of ribonuclease A involved in both the folding and unfolding pathways. Biochemistry. 33: 10437-49. PMID 8068682 DOI: 10.1021/Bi00200A027 |
0.437 |
|
| 1994 |
Liwo A, Gibson KD, Scheraga HA, Brandt-Rauf PW, Monaco R, Pincus MR. Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP. Journal of Protein Chemistry. 13: 237-51. PMID 8060496 DOI: 10.1007/Bf01891982 |
0.423 |
|
| 1994 |
Magalhaes A, Maigret B, Hoflack J, Gomes JN, Scheraga HA. Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins. Journal of Protein Chemistry. 13: 195-215. PMID 8060493 DOI: 10.1007/Bf01891978 |
0.34 |
|
| 1994 |
Dodge RW, Laity JH, Rothwarf DM, Shimotakahara S, Scheraga HA. Folding pathway of guanidine-denatured disulfide-intact wild-type and mutant bovine pancreatic ribonuclease A. Journal of Protein Chemistry. 13: 409-21. PMID 7986344 DOI: 10.1007/Bf01901697 |
0.32 |
|
| 1994 |
Nayeem A, Scheraga HA. A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions. Journal of Protein Chemistry. 13: 283-96. PMID 7945791 DOI: 10.1007/Bf01901561 |
0.421 |
|
| 1994 |
Denton ME, Rothwarf DM, Scheraga HA. Kinetics of folding of guanidine-denatured hen egg white lysozyme and carboxymethyl(Cys6,Cys127)-lysozyme: a stopped-flow absorbance and fluorescence study. Biochemistry. 33: 11225-36. PMID 7727374 DOI: 10.1021/Bi00203A019 |
0.783 |
|
| 1994 |
Allen SC, Acharya KR, Palmer KA, Shapiro R, Vallee BL, Scheraga HA. A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins. Journal of Protein Chemistry. 13: 649-58. PMID 7702747 DOI: 10.1007/Bf01890464 |
0.54 |
|
| 1994 |
Liwo A, OÅ‚dziej S, Ciarkowski J, Kupryszewski G, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Prediction of conformation of rat galanin in the presence and absence of water with the use of Monte Carlo methods and the ECEPP/3 force field. Journal of Protein Chemistry. 13: 375-80. PMID 7527217 DOI: 10.1007/Bf01901693 |
0.79 |
|
| 1994 |
Vorobjev YN, Scheraga HA, Hitz B, Honig B. Theoretical Modeling of Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in a Polar Ionic Solution. 1. Potential of Mean Force between Charged Lysine Residues and Titration of Poly(L-lysine) in 95% Methanol Solution The Journal of Physical Chemistry. 98: 10940-10948. DOI: 10.1021/J100093A042 |
0.352 |
|
| 1994 |
No KT, Cho KH, Kwon OY, Jhon MS, Scheraga HA. Determination of Proton Transfer Energies and Lattice Energies of Several Amino Acid Zwitterions The Journal of Physical Chemistry. 98: 10742-10749. DOI: 10.1021/J100093A012 |
0.312 |
|
| 1994 |
Hao M, Scheraga HA. Statistical thermodynamics of protein folding: sequence dependence The Journal of Physical Chemistry. 98: 9882-9893. DOI: 10.1021/J100090A024 |
0.329 |
|
| 1994 |
Ni F, Scheraga HA. Use of the Transferred Nuclear Overhauser Effect To Determine the Conformations of Ligands Bound to Proteins Accounts of Chemical Research. 27: 257-264. DOI: 10.1021/Ar00045A001 |
0.317 |
|
| 1994 |
Wawak RJ, Gibson KD, Scheraga HA. Gradient discontinuities in calculations involving molecular surface area Journal of Mathematical Chemistry. 15: 207-232. DOI: 10.1007/Bf01277561 |
0.328 |
|
| 1994 |
Gibson KD, Scheraga HA. A rapid and efficient algorithm for packing polypeptide chains by energy minimization Journal of Computational Chemistry. 15: 1403-1413. DOI: 10.1002/Jcc.540151210 |
0.333 |
|
| 1993 |
Rothwarf DM, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution. Biochemistry. 32: 2671-9. PMID 8448123 DOI: 10.1021/Bi00061A027 |
0.332 |
|
| 1993 |
Laity JH, Shimotakahara S, Scheraga HA. Expression of wild-type and mutant bovine pancreatic ribonuclease A in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 90: 615-9. PMID 8421696 DOI: 10.1073/Pnas.90.2.615 |
0.318 |
|
| 1993 |
Rabow AA, Scheraga HA. Lattice neural network minimization. Application of neural network optimization for locating the global-minimum conformations of proteins. Journal of Molecular Biology. 232: 1157-68. PMID 8371272 DOI: 10.1006/Jmbi.1993.1468 |
0.407 |
|
| 1993 |
Vitagliano L, Némethy G, Zagari A, Scheraga HA. Stabilization of the triple-helical structure of natural collagen by side-chain interactions. Biochemistry. 32: 7354-9. PMID 8338832 DOI: 10.1021/Bi00080A004 |
0.462 |
|
| 1993 |
Moy FJ, Li YC, Rauenbuehler P, Winkler ME, Scheraga HA, Montelione GT. Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints. Biochemistry. 32: 7334-53. PMID 8338831 DOI: 10.1021/Bi00080A003 |
0.516 |
|
| 1993 |
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide. Protein Science : a Publication of the Protein Society. 2: 1715-31. PMID 8251944 DOI: 10.1002/Pro.5560021016 |
0.801 |
|
| 1993 |
Hao MH, Pincus MR, Rackovsky S, Scheraga HA. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry. 32: 9614-31. PMID 7690589 DOI: 10.1021/Bi00088A014 |
0.797 |
|
| 1993 |
Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA. Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Science : a Publication of the Protein Society. 2: 1697-714. PMID 7504550 DOI: 10.1002/Pro.5560021015 |
0.782 |
|
| 1993 |
Talluri S, Falcomer CM, Scheraga HA. Energetic and structural basis for the preferential formation of the native disulfide loop involving Cys-65 and Cys-72 in synthetic peptide fragments derived from the sequence of ribonuclease A Journal of the American Chemical Society. 115: 3041-3047. DOI: 10.1021/Ja00061A001 |
0.362 |
|
| 1993 |
Chipot C, Angyan JG, Maigret B, Scheraga HA. Modeling amino acid side chains. 3. Influence of intra- and intermolecular environment on point charges The Journal of Physical Chemistry. 97: 9797-9807. DOI: 10.1021/J100140A043 |
0.318 |
|
| 1992 |
Montelione GT, Wüthrich K, Burgess AW, Nice EC, Wagner G, Gibson KD, Scheraga HA. Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. Biochemistry. 31: 236-49. PMID 1731873 DOI: 10.1021/Bi00116A033 |
0.659 |
|
| 1992 |
Hao MH, Rackovsky S, Liwo A, Pincus MR, Scheraga HA. Effects of compact volume and chain stiffness on the conformations of native proteins. Proceedings of the National Academy of Sciences of the United States of America. 89: 6614-8. PMID 1631164 DOI: 10.1073/Pnas.89.14.6614 |
0.807 |
|
| 1992 |
Zheng Z, Ashton RW, Ni F, Scheraga HA. Thrombin hydrolysis of an N-terminal peptide from fibrinogen Lille: kinetic and NMR studies. Biochemistry. 31: 4426-31. PMID 1581297 DOI: 10.1021/Bi00133A006 |
0.356 |
|
| 1992 |
Vila J, Williams RL, Grant JA, Wójcik J, Scheraga HA. The intrinsic helix-forming tendency of L-alanine. Proceedings of the National Academy of Sciences of the United States of America. 89: 7821-5. PMID 1502201 DOI: 10.1073/Pnas.89.16.7821 |
0.4 |
|
| 1992 |
Williams RL, Vila J, Perrot G, Scheraga HA. Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor. Proteins. 14: 110-9. PMID 1384032 DOI: 10.1002/Prot.340140112 |
0.424 |
|
| 1992 |
Chou KC, Maggiora GM, Scheraga HA. Role of loop-helix interactions in stabilizing four-helix bundle proteins. Proceedings of the National Academy of Sciences of the United States of America. 89: 7315-9. PMID 1323830 DOI: 10.1073/Pnas.89.16.7315 |
0.39 |
|
| 1992 |
Wolf RM, Francotte E, Glasser L, Simon I, Scheraga HA. Computation of low-energy crystalline arrangements of cellulose triacetate Macromolecules. 25: 709-720. DOI: 10.1021/Ma00028A033 |
0.362 |
|
| 1992 |
Kostrowicki J, Scheraga HA. Application of the diffusion equation method for global optimization to oligopeptides The Journal of Physical Chemistry. 96: 7442-7449. DOI: 10.1021/J100197A057 |
0.317 |
|
| 1992 |
Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides The Journal of Physical Chemistry. 96: 6472-6484. DOI: 10.1021/J100194A068 |
0.74 |
|
| 1992 |
Montelione GT, Wuethrich K, Burgess AW, Nice EC, Wagner G, Gibson KD, Scheraga HA. Solution structure of murine epidermal growth factor determined by NMR spectroscopy and refined by energy minimization with restraints. [Erratum to document cited in CA116(5):34702j] Biochemistry. 31: 10138-10138. DOI: 10.1021/Bi00156A038 |
0.555 |
|
| 1992 |
Moy FJ, Scheraga HA, Patt SL, Montelione GT. Application of frequency-shifted shaped pulses for overcoming solvent-saturation transfer and preirradiation-associated spin-diffusion effects in aqueous solutions of peptides and proteins Journal of Magnetic Resonance (1969). 98: 451-457. DOI: 10.1016/0022-2364(92)90147-Y |
0.466 |
|
| 1992 |
Scheraga HA. Some approaches to the multiple-minima problem in the calculation of polypeptide and protein structures International Journal of Quantum Chemistry. 42: 1529-1536. DOI: 10.1002/Qua.560420526 |
0.355 |
|
| 1992 |
Palmer KA, Scheraga HA. Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. II. Systematic searches for short loops in proteins: Applications to bovine pancreatic ribonuclease A and human lysozyme Journal of Computational Chemistry. 13: 329-350. DOI: 10.1002/Jcc.540130307 |
0.41 |
|
| 1991 |
Simon I, Glasser L, Scheraga HA. Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 88: 3661-5. PMID 2023916 DOI: 10.1073/Pnas.88.9.3661 |
0.441 |
|
| 1991 |
Denton ME, Scheraga HA. Spectroscopic, immunochemical, and thermodynamic properties of carboxymethyl(Cys6, Cys127)-hen egg white lysozyme. Journal of Protein Chemistry. 10: 213-32. PMID 1930635 DOI: 10.1007/Bf01024786 |
0.813 |
|
| 1991 |
Glasser L, Scheraga HA. Investigation of a physical basis for conformational similarity in proteins. Journal of Protein Chemistry. 10: 273-85. PMID 1910459 DOI: 10.1007/Bf01025626 |
0.384 |
|
| 1991 |
Ripoll DR, Vasquez MJ, Scheraga HA. The Electrostatically Driven Monte Carol method: Application to conformational analysis of decaglycine Biopolymers. 31: 319-330. PMID 1868160 DOI: 10.1002/Bip.360310306 |
0.408 |
|
| 1991 |
Winzor DJ, Nagy JA, Scheraga HA. Characterization of the immunochemical reactivity of fibrinogen fragments by competitive radioimmunoassay: an improved method of analysis. Journal of Protein Chemistry. 10: 629-35. PMID 1815588 DOI: 10.1007/Bf01025715 |
0.503 |
|
| 1991 |
Fossey SA, Némethy G, Gibson KD, Scheraga HA. Conformational energy studies of beta-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains. Biopolymers. 31: 1529-41. PMID 1814502 DOI: 10.1002/Bip.360311309 |
0.753 |
|
| 1991 |
Vila J, Williams RL, Vásquez M, Scheraga HA. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins. 10: 199-218. PMID 1715564 DOI: 10.1002/Prot.340100305 |
0.414 |
|
| 1991 |
Ripoll DR, Piela L, Vásquez M, Scheraga HA. On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor. Proteins. 10: 188-98. PMID 1715563 DOI: 10.1002/Prot.340100304 |
0.438 |
|
| 1991 |
Kweon GY, Scheraga HA, Jhon MS. Monte Carlo treatment of hydration of models for side chains of proteins The Journal of Physical Chemistry. 95: 8964-8968. DOI: 10.1021/J100175A098 |
0.319 |
|
| 1991 |
Kostrowicki J, Piela L, Cherayil BJ, Scheraga HA. Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms The Journal of Physical Chemistry. 95: 4113-4119. DOI: 10.1021/J100163A040 |
0.565 |
|
| 1991 |
Nayeem A, Vila J, Scheraga HA. A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-enkephalin Journal of Computational Chemistry. 12: 594-605. DOI: 10.1002/Jcc.540120509 |
0.358 |
|
| 1991 |
Palmer KA, Scheraga HA. Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. I. Chain closure through a limited search of ?loop? conformations Journal of Computational Chemistry. 12: 505-526. DOI: 10.1002/Jcc.540120410 |
0.345 |
|
| 1990 |
Moy FJ, Scheraga HA, Liu JF, Wu R, Montelione GT. Conformational characterization of a single-site mutant of murine epidermal growth factor (EGF) by 1H NMR provides evidence that leucine-47 is involved in the interactions with the EGF receptor. Proceedings of the National Academy of Sciences of the United States of America. 86: 9836-40. PMID 2690076 DOI: 10.1073/Pnas.86.24.9836 |
0.513 |
|
| 1990 |
Vásquez M, Scheraga HA. Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. Journal of Biomolecular Structure & Dynamics. 5: 757-84. PMID 2482759 DOI: 10.1080/07391102.1988.10506426 |
0.408 |
|
| 1990 |
Vásquez M, Scheraga HA. Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. Journal of Biomolecular Structure & Dynamics. 5: 705-55. PMID 2482758 DOI: 10.1080/07391102.1988.10506425 |
0.43 |
|
| 1990 |
Ni F, Konishi Y, Scheraga HA. Thrombin-bound conformation of the C-terminal fragments of hirudin determined by transferred nuclear overhauser effects Biochemistry. 29: 4479-4489. PMID 2350549 DOI: 10.1021/Bi00470A030 |
0.377 |
|
| 1990 |
Chen JM, Lee G, Brandt-Rauf PW, Murphy RB, Gibson KD, Scheraga HA, Rackovsky S, Pincus MR. Conformations of the central transforming region (Ile 55-Met 67) of the p21 protein and their relationship to activation of the protein. International Journal of Peptide and Protein Research. 36: 247-54. PMID 2279848 DOI: 10.1111/J.1399-3011.1990.Tb00975.X |
0.762 |
|
| 1990 |
Adler M, Scheraga HA. Nonnative isomers of proline-93 and -114 predominate in heat-unfolded ribonuclease A Biochemistry®. 29: 8211-8216. PMID 2252883 DOI: 10.1021/Bi00488A003 |
0.374 |
|
| 1990 |
Némethy G, Scheraga HA. Theoretical studies of protein conformation by means of energy computations. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 4: 3189-97. PMID 2227210 DOI: 10.1096/Fasebj.4.14.2227210 |
0.742 |
|
| 1990 |
Ripoll DR, Scheraga HA. On the multiple-minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven Monte Carlo method to the 20-residue membrane-bound portion of melittin. Biopolymers. 30: 165-76. PMID 2224048 DOI: 10.1002/bip.360300116 |
0.31 |
|
| 1990 |
Chou KC, Heckel A, Némethy G, Rumsey S, Carlacci L, Scheraga HA. Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins. Proteins. 8: 14-22. PMID 2217160 DOI: 10.1002/Prot.340080105 |
0.73 |
|
| 1990 |
Zagari A, Némethy G, Scheraga HA. The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. III. Collagen-like poly(tripeptide)s. Biopolymers. 30: 967-74. PMID 2092825 DOI: 10.1002/Bip.360300911 |
0.752 |
|
| 1990 |
Zagari A, Némethy G, Scheraga HA. The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. II. Homopolymers and copolymers. Biopolymers. 30: 961-6. PMID 2092824 DOI: 10.1002/Bip.360300910 |
0.729 |
|
| 1990 |
Zagari A, Némethy G, Scheraga HA. The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. I. Conformations of the residue and of dipeptides. Biopolymers. 30: 951-9. PMID 2092823 DOI: 10.1002/Bip.360300909 |
0.765 |
|
| 1990 |
Grant JA, Williams RL, Scheraga HA. Ab initio self-consistent field and potential-dependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N'-methyl-alanineamide. Biopolymers. 30: 929-49. PMID 2092822 DOI: 10.1002/Bip.360300908 |
0.364 |
|
| 1990 |
Acharya KR, Stuart DI, Phillips DC, Scheraga HA. A critical evaluation of the predicted and X-ray structures of alpha-lactalbumin. Journal of Protein Chemistry. 9: 549-63. PMID 2085380 DOI: 10.1007/Bf01025008 |
0.333 |
|
| 1990 |
Adler M, Scheraga HA. Identification of a new site of conformational heterogeneity in unfolded ribonuclease A Journal of Protein Chemistry. 9: 583-588. PMID 1964787 DOI: 10.1007/Bf01025011 |
0.438 |
|
| 1990 |
Fossey SA, Nemethy G, Gibson KD, Scheraga HA. Conformational Energy Studies of Model Silk Fibroin Peptides Mrs Proceedings. 218. DOI: 10.1557/Proc-218-253 |
0.749 |
|
| 1990 |
Meirovitch H, Vásquez M, Scheraga HA. Free energy and stability of macromolecules studied by the double scanning simulation procedure The Journal of Chemical Physics. 92: 1248-1257. DOI: 10.1063/1.458134 |
0.311 |
|
| 1990 |
Wee SS, Kim S, Jhon MS, Scheraga HA. Analytical intermolecular potential functions from ab initio SCF calculations for hydration of methylamine and methylammonium ion The Journal of Physical Chemistry. 94: 1656-1660. DOI: 10.1021/J100367A079 |
0.321 |
|
| 1990 |
Chou KC, Nemethy G, Scheraga HA. Energetics of interactions of regular structural elements in proteins Accounts of Chemical Research. 23: 134-141. DOI: 10.1021/Ar00173A003 |
0.712 |
|
| 1990 |
Gibson KD, Scheraga HA. Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles Journal of Computational Chemistry. 11: 487-492. DOI: 10.1002/Jcc.540110407 |
0.339 |
|
| 1990 |
Gibson KD, Scheraga HA. Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry Journal of Computational Chemistry. 11: 468-486. DOI: 10.1002/Jcc.540110406 |
0.344 |
|
| 1990 |
Dudek MJ, Scheraga HA. Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops Journal of Computational Chemistry. 11: 121-151. DOI: 10.1002/Jcc.540110115 |
0.344 |
|
| 1990 |
Wójcik J, Altmann K, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutylglutamine-CO-S-methylthio-L-cysteine) Biopolymers. 30: 121-134. DOI: 10.1002/Bip.360300113 |
0.326 |
|
| 1989 |
Milburn PJ, Scheraga HA. Local interactions favor the native 8-residue disulfide loop in the oxidation of a fragment corresponding to the sequence Ser-50-Met-79 derived from bovine pancreatic ribonuclease A. Journal of Protein Chemistry. 7: 377-98. PMID 3255371 DOI: 10.1007/Bf01024887 |
0.394 |
|
| 1989 |
Ripoll DR, Scheraga HA. On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine). Biopolymers. 27: 1283-303. PMID 3219397 DOI: 10.1002/Bip.360270808 |
0.408 |
|
| 1989 |
Meirovitch H, Vásquez M, Scheraga HA. Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil. Biopolymers. 27: 1189-204. PMID 3219393 DOI: 10.1002/Bip.360270802 |
0.384 |
|
| 1989 |
Chou KC, Némethy G, Pottle M, Scheraga HA. Energy of stabilization of the right-handed beta alpha beta crossover in proteins. Journal of Molecular Biology. 205: 241-9. PMID 2926804 DOI: 10.1016/0022-2836(89)90378-1 |
0.72 |
|
| 1989 |
Ray P, Moy FJ, Montelione GT, Liu JF, Narang SA, Scheraga HA, Wu R. Structure-function studies of murine epidermal growth factor: expression and site-directed mutagenesis of epidermal growth factor gene. Biochemistry. 27: 7289-95. PMID 2849989 DOI: 10.1021/Bi00419A017 |
0.468 |
|
| 1989 |
Némethy G, Scheraga HA. Free energy of hydration of collagen models and the enthalpy of the transition between the triple-helical coiled-coil and single-stranded conformations. Biopolymers. 28: 1573-84. PMID 2775848 DOI: 10.1002/Bip.360280907 |
0.745 |
|
| 1989 |
Robertson AD, Purisima EO, Eastman MA, Scheraga HA. Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution Biochemistry. 28: 5930-5938. PMID 2775743 DOI: 10.1021/Bi00440A033 |
0.62 |
|
| 1989 |
Ni F, Konishi Y, Bullock LD, Rivetna MN, Scheraga HA. High-resolution NMR studies of fibrinogen-like peptides in solution: structural basis for the bleeding disorder caused by a single mutation of Gly(12) to Val(12) in the A alpha chain of human fibrinogen Rouen. Biochemistry. 28: 3106-19. PMID 2742828 DOI: 10.1021/Bi00433A054 |
0.373 |
|
| 1989 |
Ni F, Meinwald YC, Vásquez M, Scheraga HA. High-resolution NMR studies of fibrinogen-like peptides in solution: structure of a thrombin-bound peptide corresponding to residues 7-16 of the A alpha chain of human fibrinogen. Biochemistry. 28: 3094-105. PMID 2742827 DOI: 10.1021/Bi00433A053 |
0.356 |
|
| 1989 |
Ni F, Konishi Y, Frazier RB, Scheraga HA, Lord ST. High-resolution NMR studies of fibrinogen-like peptides in solution: interaction of thrombin with residues 1-23 of the A alpha chain of human fibrinogen. Biochemistry. 28: 3082-94. PMID 2742826 DOI: 10.1021/Bi00433A052 |
0.315 |
|
| 1989 |
Ripoll DR, Scheraga HA. The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin. Journal of Protein Chemistry. 8: 263-87. PMID 2736043 DOI: 10.1007/Bf01024949 |
0.448 |
|
| 1989 |
Jernigan R, Davies D, Scheraga H. Experimental and theoretical protein folding. Journal of Biomolecular Structure & Dynamics. 6: 1039-43. PMID 2684216 DOI: 10.1080/07391102.1989.10506534 |
0.334 |
|
| 1989 |
Roterman IK, Lambert MH, Gibson KD, Scheraga HA. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. ϕ-ψ maps for n-acetyl alanine n’-methyl amide: Comparisons, contrasts and simple experimental tests Journal of Biomolecular Structure and Dynamics. 7: 421-453. PMID 2627294 DOI: 10.1080/07391102.1989.10508503 |
0.303 |
|
| 1989 |
Roterman IK, Gibson KD, Scheraga HA. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (asn-ala-asn-pro)9 Journal of Biomolecular Structure and Dynamics. 7: 391-419. PMID 2627293 DOI: 10.1080/07391102.1989.10508502 |
0.424 |
|
| 1989 |
Shah D, Chen JM, Carty RP, Pincus MR, Scheraga HA. Correlation of beta-bend conformations of tetrapeptides with their activities in CD4-receptor binding assays. International Journal of Peptide and Protein Research. 34: 325-32. PMID 2599773 DOI: 10.1111/J.1399-3011.1989.Tb01582.X |
0.365 |
|
| 1989 |
Montelione GT, Scheraga HA. Formation of local structures in protein folding Accounts of Chemical Research. 22: 70-76. DOI: 10.1021/Ar00158A004 |
0.513 |
|
| 1989 |
Lambert MH, Scheraga HA. Pattern recognition in the prediction of protein structure. III. An importance-sampling minimization procedure Journal of Computational Chemistry. 10: 817-831. DOI: 10.1002/Jcc.540100605 |
0.418 |
|
| 1989 |
Lambert MH, Scheraga HA. Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability-directed search procedure Journal of Computational Chemistry. 10: 798-816. DOI: 10.1002/Jcc.540100604 |
0.41 |
|
| 1989 |
Lambert MH, Scheraga HA. Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence Journal of Computational Chemistry. 10: 770-797. DOI: 10.1002/Jcc.540100603 |
0.385 |
|
| 1989 |
Kikuchi T, Némethy G, Scheraga HA. Spatial geometric arrangements of disulfide-crosslinked loops in nonplanar proteins Journal of Computational Chemistry. 10: 287-294. DOI: 10.1002/Jcc.540100302 |
0.731 |
|
| 1988 |
Purisima EO, Scheraga HA. An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin. Journal of Molecular Biology. 196: 697-709. PMID 3681972 DOI: 10.1016/0022-2836(87)90041-6 |
0.659 |
|
| 1988 |
Swadesh JK, Mui PW, Scheraga HA. Thermodynamics of the quenching of tyrosyl fluorescence by dithiothreitol. Biochemistry. 26: 5761-9. PMID 3676287 DOI: 10.1021/Bi00392A027 |
0.313 |
|
| 1988 |
Adler M, Scheraga HA. Structural studies of a folding intermediate of bovine pancreatic ribonuclease a by continuous recycled flow Biochemistry®. 27: 2471-2480. PMID 3382634 DOI: 10.1021/Bi00407A033 |
0.404 |
|
| 1988 |
Chou KC, Maggiora GM, Némethy G, Scheraga HA. Energetics of the structure of the four-alpha-helix bundle in proteins. Proceedings of the National Academy of Sciences of the United States of America. 85: 4295-9. PMID 3380793 DOI: 10.1073/Pnas.85.12.4295 |
0.744 |
|
| 1988 |
Milburn PJ, Meinwald YC, Takahashi S, Ooi T, Scheraga HA. Chain reversals in model peptides: studies of cystine-containing cyclic peptides. II. Effects of valyl residues and possible i-to-(i + 3) attractive ionic interactions on cyclization of [Cys1], [Cys6] hexapeptides. International Journal of Peptide and Protein Research. 31: 311-21. PMID 3372134 DOI: 10.1111/J.1399-3011.1988.Tb00039.X |
0.356 |
|
| 1988 |
Glasser L, Scheraga HA. Calculations on crystal packing of a flexible molecule, Leu-enkephalin. Journal of Molecular Biology. 199: 513-24. PMID 3351940 DOI: 10.1016/0022-2836(88)90622-5 |
0.341 |
|
| 1988 |
Vásquez M, Scheraga HA. Effect of sequence-specific interactions on the stability of helical conformations in polypeptides. Biopolymers. 27: 41-58. PMID 3342277 DOI: 10.1002/Bip.360270104 |
0.343 |
|
| 1988 |
Haas E, McWherter CA, Scheraga HA. Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer: distribution of interresidue distances in the native, denatured, and reduced-denatured states Biopolymers - Peptide Science Section. 27: 1-21. PMID 3342273 DOI: 10.1002/Bip.360270102 |
0.346 |
|
| 1988 |
Kikuchi T, Némethy G, Scheraga HA. Prediction of probable pathways of folding in globular proteins. Journal of Protein Chemistry. 7: 491-507. PMID 3255374 DOI: 10.1007/Bf01024892 |
0.742 |
|
| 1988 |
Kikuchi T, Némethy G, Scheraga HA. Prediction of the packing arrangement of strands in beta-sheets of globular proteins. Journal of Protein Chemistry. 7: 473-90. PMID 3255373 DOI: 10.1007/Bf01024891 |
0.743 |
|
| 1988 |
Kikuchi T, Némethy G, Scheraga HA. Prediction of the location of structural domains in globular proteins. Journal of Protein Chemistry. 7: 427-71. PMID 3255372 DOI: 10.1007/Bf01024890 |
0.746 |
|
| 1988 |
Ni F, Scheraga HA, Lord ST. High-resolution NMR studies of fibrinogen-like peptides in solution: resonance assignments and conformational analysis of residues 1-23 of the A alpha chain of human fibrinogen. Biochemistry. 27: 4481-91. PMID 3166991 DOI: 10.1021/Bi00412A040 |
0.361 |
|
| 1988 |
Pincus MR, Murphy RB, Carty RP, Chen J, Shah D, Scheraga HA. Conformational analysis of possible biologically active (receptor-bound) conformations of peptides derived from cholecystokinin, cerulein and little gastrin and the opiate peptide, Met-enkephalin. Peptides. 9: 145-52. PMID 2856638 DOI: 10.1016/0196-9781(88)90238-0 |
0.328 |
|
| 1988 |
Montelione GT, Wüthrich K, Scheraga HA. Sequence-specific 1H NMR assignments and identification of slowly exchanging amide protons in murine epidermal growth factor. Biochemistry. 27: 2235-43. PMID 2837287 DOI: 10.1021/bi00406a064 |
0.582 |
|
| 1988 |
Mattice WL, Nemethy G, Scheraga HA. Conformational entropy associated with the formation of internal loops in collagen Macromolecules. 21: 2811-2818. DOI: 10.1021/Ma00187A029 |
0.716 |
|
| 1988 |
Simon I, Glasser L, Scheraga HA, Manley RSJ. Structure of cellulose. 2. Low-energy crystalline arrangements Macromolecules. 21: 990-998. DOI: 10.1021/Ma00182A025 |
0.398 |
|
| 1988 |
Simon I, Scheraga HA, Manley RSJ. Structure of cellulose. 1. Low-energy conformations of single chains Macromolecules. 21: 983-990. DOI: 10.1021/Ma00182A024 |
0.398 |
|
| 1988 |
Kim S, Jhon MS, Scheraga HA. Analytic intermolecular potential functions from ab initio SCF calculations of interaction energies between methane, methanol, acetic acid, and acetate and water The Journal of Physical Chemistry. 92: 7216-7223. DOI: 10.1021/J100337A012 |
0.312 |
|
| 1988 |
Kang YK, Gibson KD, Nemethy G, Scheraga HA. Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model The Journal of Physical Chemistry. 92: 4739-4742. DOI: 10.1021/J100327A036 |
0.696 |
|
| 1988 |
Li Z, Scheraga HA. Structure and free energy of complex thermodynamic systems Journal of Molecular Structure: Theochem. 179: 333-352. DOI: 10.1016/0166-1280(88)80133-7 |
0.352 |
|
| 1987 |
Piela L, Némethy G, Scheraga HA. Proline-induced constraints in alpha-helices. Biopolymers. 26: 1587-600. PMID 3663874 DOI: 10.1002/Bip.360260910 |
0.683 |
|
| 1987 |
Piela L, Nemethy G, Scheraga HA. Conformational constraints of amino acid side chains in alpha-helices. Biopolymers. 26: 1273-86. PMID 3663860 DOI: 10.1002/Bip.360260805 |
0.759 |
|
| 1987 |
Thannhauser TW, Konishi Y, Scheraga HA. Analysis for disulfide bonds in peptides and proteins. Methods in Enzymology. 143: 115-9. PMID 3657523 DOI: 10.1016/0076-6879(87)43020-6 |
0.357 |
|
| 1987 |
Paine GH, Scheraga HA. Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. III. Probable and average conformations of enkephalin. Biopolymers. 26: 1125-62. PMID 3620578 DOI: 10.1002/Bip.360260711 |
0.457 |
|
| 1987 |
Meirovitch H, Vásquez M, Scheraga HA. Stability of polypeptide conformational states as determined by computer simulation of the free energy. Biopolymers. 26: 651-71. PMID 3593889 DOI: 10.1002/Bip.360260508 |
0.432 |
|
| 1987 |
Haas E, Montelione GT, McWherter CA, Scheraga HA. Local structure in a tryptic fragment of performic acid oxidized ribonuclease A corresponding to a proposed polypeptide chain-folding initiation site detected by tyrosine fluorescence lifetime and proton magnetic resonance measurements Biochemistry. 26: 1672-1683. PMID 3593685 DOI: 10.1021/Bi00380A028 |
0.509 |
|
| 1987 |
Piela L, Scheraga HA. On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed alpha-helix. Biopolymers. S33-58. PMID 3580500 DOI: 10.1002/Bip.360260008 |
0.388 |
|
| 1987 |
Vasquez M, Pincus MR, Scheraga HA. Helix-coil transition theory including long-range electrostatic interactions: application to globular proteins. Biopolymers. 26: 351-71. PMID 3567318 DOI: 10.1002/Bip.360260305 |
0.379 |
|
| 1987 |
Montelione GT, Wüthrich K, Nice EC, Burgess AW, Scheraga HA. Solution structure of murine epidermal growth factor: determination of the polypeptide backbone chain-fold by nuclear magnetic resonance and distance geometry. Proceedings of the National Academy of Sciences of the United States of America. 84: 5226-30. PMID 3496602 DOI: 10.1073/Pnas.84.15.5226 |
0.581 |
|
| 1987 |
Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proceedings of the National Academy of Sciences of the United States of America. 84: 6611-5. PMID 3477791 DOI: 10.1073/Pnas.84.19.6611 |
0.375 |
|
| 1987 |
Scheraga HA, Konishi Y, Rothwarf DM, Mui PW. Toward an understanding of the folding of ribonuclease A. Proceedings of the National Academy of Sciences of the United States of America. 84: 5740-4. PMID 3475701 DOI: 10.1073/Pnas.84.16.5740 |
0.306 |
|
| 1987 |
Ooi T, Oobatake M, Némethy G, Scheraga HA. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proceedings of the National Academy of Sciences of the United States of America. 84: 3086-90. PMID 3472198 DOI: 10.1073/Pnas.84.10.3086 |
0.716 |
|
| 1987 |
Pincus MR, Brandt-Rauf PW, Carty RP, Lubowsky J, Avitable M, Gibson KD, Scheraga HA. Conformational effects of substituting amino acids for glutamine-61 on the central transforming region of the P21 proteins Proceedings of the National Academy of Sciences of the United States of America. 84: 8375-8379. PMID 3120190 DOI: 10.1073/Pnas.84.23.8375 |
0.349 |
|
| 1987 |
Takahashi K, Kang YK, Némethy G, Scheraga HA, Ananthanarayanan VS. Low-energy conformations of two lysine-containing tetrapeptides of collagen: implications for posttranslational lysine hydroxylation. Biopolymers. 26: 1781-8. PMID 3117128 DOI: 10.1002/Bip.360261010 |
0.746 |
|
| 1987 |
Pincus MR, Carty RP, Chen J, Lubowsky J, Avitable M, Shah D, Scheraga HA, Murphy RB. On the biologically active structures of cholecystokinin, little gastrin, and enkephalin in the gastrointestinal system. Proceedings of the National Academy of Sciences of the United States of America. 84: 4821-5. PMID 3037525 DOI: 10.1073/Pnas.84.14.4821 |
0.38 |
|
| 1987 |
Vasquez M, Pincus MR, Scheraga HA. Correlation between computed conformational properties of cytochrome c peptides and their antigenicity in a T-lymphocyte proliferation assay. Biopolymers. 26: 373-86. PMID 3032295 DOI: 10.1002/Bip.360260306 |
0.373 |
|
| 1987 |
Piela L, Nemethy G, Scheraga HA. Conformational properties of 2,4-methanoproline (2-carboxy-2,4-methanopyrrolidine) in peptides: theoretical conformational energy analysis of restrictions of the polypeptide chain conformation Journal of the American Chemical Society. 109: 4477-4485. DOI: 10.1021/Ja00249A009 |
0.75 |
|
| 1987 |
Talluri S, Montelione GT, Van Duyne G, Piela L, Clardy J, Scheraga HA. Conformational properties of 2,4-methanoproline (2-carboxy-2,4-methanopyrrolidine) in peptides: evidence for 2,4-methanopyrrolidine asymmetry based on solid-state x-ray crystallography, proton NMR in aqueous solution, and CNDO/2 conformational energy calculations Journal of the American Chemical Society. 109: 4473-4477. DOI: 10.1021/Ja00249A008 |
0.525 |
|
| 1987 |
Milburn P, Konishi Y, Meinwald Y, Scheraga H. Correction. Chain Reversals in Model Peptides: Studies of Cystine-Containing Cyclic Peptides. 1. Conformational Free Energies of Cyclization of Hexapeptides of Sequence Ac-Cys-X-Pro-Gly-Y-Cys-NHMe Journal of the American Chemical Society. 109: 8123-8123. DOI: 10.1021/Ja00037A003 |
0.334 |
|
| 1987 |
Meirovitch E, Samulski ET, Leed A, Scheraga HA, Rananavare S, Nemethy G, Freed JH. Deuterium NMR study of the structure and dynamic of the side chains of several solid polyglutamates The Journal of Physical Chemistry. 91: 4840-4851. DOI: 10.1021/J100302A038 |
0.705 |
|
| 1987 |
Kang YK, Nemethy G, Scheraga HA. Free energies of hydration of solute molecules. 3. Application of the hydration shell model to charged organic molecules The Journal of Physical Chemistry. 91: 4118-4120. DOI: 10.1021/J100299A034 |
0.698 |
|
| 1987 |
Kang YK, Nemethy G, Scheraga HA. Free energies of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes The Journal of Physical Chemistry. 91: 4105-4109. DOI: 10.1021/J100299A032 |
0.702 |
|
| 1987 |
Némethy G, Ooi T, Scheraga HA. Structural principles of protein architecture Journal of Protein Chemistry. 6: 529-535. DOI: 10.1007/Bf00276738 |
0.359 |
|
| 1987 |
Gibson KD, Scheraga HA. Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization Journal of Computational Chemistry. 8: 826-834. DOI: 10.1002/Jcc.540080611 |
0.359 |
|
| 1987 |
PIELA L, NEMETHY G, SCHERAGA HA. ChemInform Abstract: Conformational Properties of 2,4-Methanoproline (2-Carboxy-2,4-methanopyrrolidine) in Peptides: Theoretical Conformational Energy Analysis of Restrictions of the Polypeptide Chain Conformation Cheminform. 18. DOI: 10.1002/chin.198746337 |
0.732 |
|
| 1987 |
KANG YK, NEMETHY G, SCHERAGA HA. ChemInform Abstract: Free Energies of Hydration of Solute Molecules. Part 2. Application of the Hydration Shell Model to Nonionic Organic Molecules. Cheminform. 18. DOI: 10.1002/chin.198745068 |
0.671 |
|
| 1987 |
KANG YK, NEMETHY G, SCHERAGA HA. ChemInform Abstract: Free Energies of Hydration of Solute Molecules. Part 1. Improvement of the Hydration Shell Model by Exact Computations of Overlapping Volumes. Cheminform. 18. DOI: 10.1002/chin.198745067 |
0.681 |
|
| 1986 |
Thannhauser TW, Scheraga HA. Reversible blocking of half-cystine residues of proteins and an irreversible specific deamidation of asparagine-67 of S-sulforibonuclease under mild conditions. Biochemistry. 24: 7681-8. PMID 4092033 DOI: 10.1021/Bi00347A027 |
0.34 |
|
| 1986 |
Thannhauser TW, McWherter CA, Scheraga HA. Peptide mapping of bovine pancreatic ribonuclease A by reverse-phase high-performance liquid chromatography. II. A two-dimensional technique for determination of disulfide pairings using a continuous-flow disulfide-detection system. Analytical Biochemistry. 149: 322-30. PMID 3907407 DOI: 10.1016/0003-2697(85)90577-9 |
0.311 |
|
| 1986 |
Meinwald YC, Stimson ER, Scheraga HA. Deamidation of the asparaginyl-glycyl sequence. International Journal of Peptide and Protein Research. 28: 79-84. PMID 3759344 DOI: 10.1111/J.1399-3011.1986.Tb03231.X |
0.312 |
|
| 1986 |
Stimson ER, Meinwald YC, Montelione GT, Scheraga HA. Conformational properties of trans Ac-Asn-Pro-Tyr-NHMe and trans Ac-Tyr-Pro-Asn-NHMe in dimethylsulfoxide and in water determined by multinuclear n.m.r. spectroscopy. International Journal of Peptide and Protein Research. 27: 569-82. PMID 3759333 DOI: 10.1111/J.1399-3011.1986.Tb01052.X |
0.55 |
|
| 1986 |
Chou KC, Némethy G, Rumsey S, Tuttle RW, Scheraga HA. Interactions between two beta-sheets. Energetics of beta/beta packing in proteins. Journal of Molecular Biology. 188: 641-9. PMID 3755478 DOI: 10.1016/S0022-2836(86)80012-2 |
0.707 |
|
| 1986 |
Eastman MA, Pedersen LG, Hiskey RG, Pique M, Koehler KA, Gottschalk KE, Némethy G, Scheraga HA. Conformation of the 18-23 loop region of bovine prothrombin in the absence and presence of a model Ca2+ ion. An energy minimization study. International Journal of Peptide and Protein Research. 27: 530-53. PMID 3733321 |
0.729 |
|
| 1986 |
Némethy G, Scheraga HA. Stabilization of collagen fibrils by hydroxyproline. Biochemistry. 25: 3184-8. PMID 3730354 DOI: 10.1021/Bi00359A016 |
0.744 |
|
| 1986 |
Montelione GT, Wüthrich K, Nice EC, Burgess AW, Scheraga HA. Identification of two anti-parallel beta-sheet conformations in the solution structure of murine epidermal growth factor by proton magnetic resonance. Proceedings of the National Academy of Sciences of the United States of America. 83: 8594-8. PMID 3490668 DOI: 10.1073/Pnas.83.22.8594 |
0.61 |
|
| 1986 |
Scheraga HA, Paine GH. Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties. Annals of the New York Academy of Sciences. 482: 60-8. PMID 3471114 DOI: 10.1111/J.1749-6632.1986.Tb20937.X |
0.444 |
|
| 1986 |
Purisima EO, Scheraga HA. An approach to the multiple-minima problem by relaxing dimensionality. Proceedings of the National Academy of Sciences of the United States of America. 83: 2782-6. PMID 3458240 DOI: 10.1073/Pnas.83.9.2782 |
0.634 |
|
| 1986 |
Van Wart HE, Scheraga HA. Agreement with the disulfide stretching frequency-conformation correlation of Sugeta, Go, and Miyazawa. Proceedings of the National Academy of Sciences of the United States of America. 83: 3064-7. PMID 3458164 DOI: 10.1073/Pnas.83.10.3064 |
0.636 |
|
| 1986 |
Palmer KA, Scheraga HA, Riordan JF, Vallee BL. A preliminary three-dimensional structure of angiogenin Proceedings of the National Academy of Sciences of the United States of America. 83: 1965-1969. PMID 3457369 DOI: 10.1073/Pnas.83.7.1965 |
0.56 |
|
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