Harold Abraham Scheraga - Publications

Affiliations: 
1947- Cornell University, Ithaca, NY, United States 
Area:
structures of proteins
Website:
http://chemistry.cornell.edu/faculty/detail.cfm?netid=has5

385 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.8
2018 Rojas AV, Maisuradze GG, Scheraga HA. Formation of Tau and Aβ Peptide Mixed Aggregates Depends on the Secondary Structure of the N-Terminal Region of Aβ. The Journal of Physical Chemistry. B. PMID 29940109 DOI: 10.1021/acs.jpcb.8b04647  0.56
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  0.56
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  0.56
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  0.92
2017 Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. Journal of Chemical Information and Modeling. PMID 29283263 DOI: 10.1021/acs.jcim.7b00716  0.76
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  0.76
2017 Vila JA, Scheraga HA. Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. Journal of Molecular Structure. 1134: 576-581. PMID 28919647 DOI: 10.1016/j.molstruc.2017.01.022  0.44
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  0.44
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  0.76
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  1
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  0.44
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  0.56
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  0.76
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  0.56
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  1
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  0.8
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  0.76
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  1
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  0.8
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  1
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  0.76
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  0.8
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  0.76
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  1
2015 Scheraga HA. My 65 years in protein chemistry. Quarterly Reviews of Biophysics. 48: 117-77. PMID 25850343 DOI: 10.1017/S0033583514000134  1
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  1
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  0.76
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  0.76
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  1
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  1
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: Structure, Function and Bioinformatics. DOI: 10.1002/prot.24824  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 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 M, Sieradzan A, Smadbeck J, ... ... Scheraga HA, et al. Wefold: A collaborative protein structure prediction experiment Computational Molecular Science and Engineering Forum 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 182-184.  1
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  1
2012 Makowska J, Liwo A, Chmurzy?ski L, Scheraga HA. Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5). Journal of Solution Chemistry. 41: 1738-1746. PMID 23204596 DOI: 10.1007/s10953-012-9903-7  1
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  1
2012 Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ. CheShift-2 resolves a local inconsistency between two X-ray crystal structures. Journal of Biomolecular Nmr. 54: 193-8. PMID 22945426 DOI: 10.1007/s10858-012-9663-0  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Makowska J, Liwo A, ZmudziÅ„ska W, Lewandowska A, ChmurzyÅ„ski 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  1
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  1
2012 O?dziej S, Czaplewski C, Liwo A, Vila JA, Scheraga HA. Computation of structure, dynamics, and thermodynamics of proteins Comprehensive Biophysics. 1: 494-513. DOI: 10.1016/B978-0-12-374920-8.00126-0  1
2012 Scheraga HA. Personal perspective Rsc Biomolecular Sciences. 1: 3-7.  1
2011 Bardwell DA, Adjiman CS, Arnautova YA, Bartashevich E, Boerrigter SX, Braun DE, Cruz-Cabeza AJ, Day GM, Della Valle RG, Desiraju GR, van Eijck BP, Facelli JC, Ferraro MB, Grillo D, Habgood M, ... ... Scheraga HA, et al. Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. Acta Crystallographica. Section B, Structural Science. 67: 535-51. PMID 22101543 DOI: 10.1107/S0108768111042868  1
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  1
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  1
2011 Scheraga HA. Respice, adspice, and prospice. Annual Review of Biophysics. 40: 1-39. PMID 21545283 DOI: 10.1146/annurev-biophys-042910-155334  1
2011 Makowski M, Liwo A, Sobolewski E, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. The Journal of Physical Chemistry. B. 115: 6119-29. PMID 21500792 DOI: 10.1021/jp111258p  1
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  1
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  1
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  1
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  1
2011 Czaplewski C, Liwo A, Makowski M, O?dziej S, Scheraga HA. Coarse-grained models of proteins: Theory and applications Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies. 35-83. DOI: 10.1007/978-1-4419-6889-0_3  1
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  1
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  1
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  1
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  0.44
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  1
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  1
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  1
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  1
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  1
2010 KozÅ‚owska 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  1
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  1
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  1
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  1
2010 KozÅ‚owska 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  1
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  1
2010 O?dziej S, Czaplewski C, Liwo A, Scheraga HA. Towards temperature dependent coarse-grained potential of side-chain interactions for protein folding simulations II. Simple functional forms for the side-chain-interaction potential: Effect on simulated heat capacity and radius of gyration of staphylococcal protein A 10th Ieee International Conference On Bioinformatics and Bioengineering 2010, Bibe 2010. 263-266. DOI: 10.1109/BIBE.2010.50  1
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  1
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  0.36
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  1
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  1
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  1
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  1
2009 Sobolewski E, Makowski M, Oldziej S, Czaplewski C, Liwo A, Scheraga HA. Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures. Protein Engineering, Design & Selection : Peds. 22: 547-52. PMID 19556395 DOI: 10.1093/protein/gzp028  1
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  1
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  1
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  1
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  1
2009 Day GM, Cooper TG, Cruz-Cabeza AJ, Hejczyk KE, Ammon HL, Boerrigter SX, Tan JS, Della Valle RG, Venuti E, Jose J, Gadre SR, Desiraju GR, Thakur TS, van Eijck BP, Facelli JC, ... ... Scheraga HA, et al. Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallographica. Section B, Structural Science. 65: 107-25. PMID 19299868 DOI: 10.1107/S0108768109004066  1
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  1
2009 Skwierawska A, ZmudziÅ„ska W, 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. 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  1
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  1
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  1
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  1
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  1
2008 Shen H, Czaplewski C, Liwo A, Scheraga HA. Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field. Journal of Chemical Theory and Computation. 4: 1386-1400. PMID 20011673 DOI: 10.1021/ct800063d  1
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  1
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  1
2008 Makowska J, BagiÅ„ska K, Skwierawska A, Liwo A, ChmurzyÅ„ski 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  1
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  1
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  1
2008 Skwierawska A, Rodziewicz-MotowidÅ‚o S, OÅ‚dziej 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  1
2008 Makowska J, BagiÅ„ska K, Liwo A, ChmurzyÅ„ski 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  1
2008 Kleinerman DS, Czaplewski C, Liwo A, Scheraga HA. Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain. The Journal of Chemical Physics. 128: 245103. PMID 18601387 DOI: 10.1063/1.2943146  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Scheraga HA. From helix-coil transitions to protein folding. Biopolymers. 89: 479-85. PMID 18008324 DOI: 10.1002/bip.20890  1
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  1
2008 Niv MY, Skrabanek L, Roberts RJ, Scheraga HA, Weinstein H. Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints. Proteins. 71: 631-40. PMID 17972284 DOI: 10.1002/prot.21777  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2007 Makowski M, Liwo A, Maksimiak K, Makowska J, Scheraga HA. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. The Journal of Physical Chemistry. B. 111: 2917-24. PMID 17388417 DOI: 10.1021/jp065917k  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2007 Kozłowska 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  1
2007 Scheraga HA. Experimental and theoretical aspects of protein folding and hydrophobic interactions Proceedings of the International School of Physics "Enrico Fermi". 165: 1-25.  1
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  1
2006 Rakowski F, Grochowski P, Lesyng B, Liwo A, Scheraga HA. Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. The Journal of Chemical Physics. 125: 204107. PMID 17144690 DOI: 10.1063/1.2399526  1
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  1
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  1
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  1
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  1
2006 Makowska J, Rodziewicz-MotowidÅ‚o S, BagiÅ„ska K, Vila JA, Liwo A, ChmurzyÅ„ski 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  1
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  1
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  1
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  1
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  1
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.  1
2005 Shimizu S, Moghaddam MS, Chan HS, Czaplewski C, Kalinowski S, Liwo A, Ripoll DR, Scheraga HA. Comment on "molecular origin of anticooperativity in hydrophobic Association" Journal of Physical Chemistry B. 109: 21220-21224. PMID 16853749 DOI: 10.1021/jp052076t  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 OÅ‚dziej 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  1
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  1
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  1
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  1
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  1
2005 Makowska J, BagiÅ„ska K, Kasprzykowski F, Vila JA, Jagielska A, Liwo A, ChmurzyÅ„ski 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  1
2005 Czaplewski C, Kalinowski S, Liwo A, Scheraga HA. Comparison of two approaches to potential of mean force calculations of hydrophobic association: Particle insertion and weighted histogram analysis methods Molecular Physics. 103: 3153-3167. DOI: 10.1080/00268970500233797  1
2004 Jang SH, Kang DK, Chang SI, Scheraga HA, Shin HC. High level production of bovine angiogenin in E. coli by an efficient refolding procedure. Biotechnology Letters. 26: 1501-4. PMID 15604787 DOI: 10.1023/B:BILE.0000044452.57375.fb  1
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  1
2004 Scheraga HA. The thrombin-fibrinogen interaction. Biophysical Chemistry. 112: 117-30. PMID 15572239 DOI: 10.1016/j.bpc.2004.07.011  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Fernández A, Rogale K, Scott R, Scheraga HA. Inhibitor design by wrapping packing defects in HIV-1 proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 11640-5. PMID 15289598 DOI: 10.1073/pnas.0404641101  1
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  1
2004 Kamikubo Y, De Guzman R, Kroon G, Curriden S, Neels JG, Churchill MJ, Dawson P, OÅ‚dziej S, Jagielska A, Scheraga HA, Loskutoff DJ, Dyson HJ. Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin. Biochemistry. 43: 6519-34. PMID 15157085 DOI: 10.1021/bi049647c  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Liwo A, Ołdziej S, Czaplewski C, Kozłowska 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  1
2004 Griffith JH, Scheraga HA. Statistical thermodynamics of aqueous solutions II. Alkali halides at infinite dilution Journal of Molecular Structure: Theochem. 711: 33-48. DOI: 10.1016/j.theochem.2004.08.008  1
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  1
2004 Czaplewski C, Liwo A, Pillardy J, Ołdziej 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  1
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  1
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  1
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  1
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  1
2003 Czaplewski C, Rodziewicz-MotowidÅ‚o S, Dabal M, Liwo A, Ripoll DR, Scheraga HA. Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles. Biophysical Chemistry. 105: 339-59. PMID 14499903 DOI: 10.1016/S0301-4622(03)00085-1  1
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  1
2003 Narayan M, Welker E, Scheraga HA. Characterizing the unstructured intermediates in oxidative folding. Biochemistry. 42: 6947-55. PMID 12795589 DOI: 10.1021/bi030054w  1
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  1
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  1
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  0.76
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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.  1
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.  1
2003 Vila JA, Ripoll DR, Baldoni HA, Scheraga HA. Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: A theoretical study (Journal of Biomolecular NMR (2002) vol. 24 (245-262)) Journal of Biomolecular Nmr. 25: 171.  1
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  0.48
2002 Scheraga HA, Vila JA, Ripoll DR. Helix-coil transitions re-visited. Biophysical Chemistry. 101: 255-65. PMID 12488006  0.48
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  0.48
2002 Wedemeyer WJ, Welker E, Scheraga HA. Proline cis-trans isomerization and protein folding. Biochemistry. 41: 14637-44. PMID 12475212 DOI: 10.1021/bi020574b  1
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  1
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  1
2002 Welker E, Raymond LD, Scheraga HA, Caughey B. Intramolecular versus intermolecular disulfide bonds in prion proteins. The Journal of Biological Chemistry. 277: 33477-81. PMID 12082114 DOI: 10.1074/jbc.M204273200  1
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  1
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  0.76
2002 Saunders JA, Gibson KD, Scheraga HA. Ab initio folding of multiple-chain proteins. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 601-12. PMID 11928512  1
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  1
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  1
2002 Liwo A, ArÅ‚ukowicz P, Czaplewski C, OÅ‚dziej 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  0.76
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.48
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  1
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  1
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  1
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  0.48
2000 Czaplewski C, Rodziewicz-MotowidÅ‚o 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  0.76
2000 Wedemeyer WJ, Welker E, Narayan M, Scheraga HA. Disulfide bonds and protein folding Biochemistry. 39: 7032. PMID 10841785  1
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  1
2000 Wedemeyer WJ, Welker E, Narayan M, Scheraga HA. Disulfide bonds and protein folding. Biochemistry. 39: 4207-16. PMID 10757967 DOI: 10.1021/bi992922o  1
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  1
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  0.4
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  0.48
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  1
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  0.76
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  0.48
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  0.48
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  1
1999 Hao MH, Scheraga HA. Designing potential energy functions for protein folding. Current Opinion in Structural Biology. 9: 184-8. PMID 10322206  0.44
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  0.76
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  1
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  0.76
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  1
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  0.48
1998 Juminaga D, Wedemeyer WJ, Scheraga HA. Proline isomerization in bovine pancreatic ribonuclease A. 1. Unfolding conditions. Biochemistry. 37: 11614-20. PMID 9708999 DOI: 10.1021/bi981028e  1
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  0.76
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  1
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  1
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  1
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  1
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  0.44
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  1
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  0.6
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  0.6
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  1
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  1
1997 Juminaga D, Wedemeyer WJ, Garduño-Júarez R, McDonald MA, Scheraga HA. Tyrosyl interactions in the folding and unfolding of bovine pancreatic ribonuclease A: a study of tyrosine-to-phenylalanine mutants. Biochemistry. 36: 10131-45. PMID 9254610 DOI: 10.1021/bi970711i  1
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  0.48
1997 Wedemeyer WJ, Ashton RW, Scheraga HA. Kinetics of competitive binding with application to thrombin complexes. Analytical Biochemistry. 248: 130-40. PMID 9177732 DOI: 10.1006/abio.1997.2087  1
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  0.6
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  0.48
1996 Wawak RJ, Gibson KD, Liwo A, Scheraga HA. Theoretical prediction of a crystal structure. Proceedings of the National Academy of Sciences of the United States of America. 93: 1743-6. PMID 11607635 DOI: 10.1073/pnas.93.5.1743  1
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  1
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  0.76
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  0.6
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  1
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  1
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  1
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  1
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  1
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  1
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  0.6
1996 DiBella EE, Scheraga HA. The role of the insertion loop around tryptophan 148 in tthe activity of thrombin. Biochemistry. 35: 4427-33. PMID 8605192 DOI: 10.1021/bi952617c  1
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  1
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  1
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  1
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  1
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  1
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  1
1995 Ashton RW, Scheraga HA. Preparation and characterization of anhydrothrombin. Biochemistry. 34: 6454-63. PMID 7756277  1
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  1
1995 Li YJ, Rothwarf DM, Scheraga HA. Mechanism of reductive protein unfolding. Nature Structural Biology. 2: 489-94. PMID 7664112  0.6
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  1
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  1
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  1
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  0.6
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  1
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  0.6
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  0.96
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  1
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  1
1993 Buckler DR, Haas E, Scheraga HA. C-terminal labeling of ribonuclease A with an extrinsic fluorescent probe by carboxypeptidase Y-catalyzed transpeptidation in the presence of urea. Analytical Biochemistry. 209: 20-31. PMID 8465956 DOI: 10.1006/abio.1993.1078  1
1993 Rothwarf DM, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A. 4. Temperature dependence of the regeneration rate. Biochemistry. 32: 2698-703. PMID 8448126  0.6
1993 Rothwarf DM, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A. 3. Dependence on the nature of the redox reagent. Biochemistry. 32: 2690-7. PMID 8448125  0.6
1993 Rothwarf DM, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A. 2. Kinetics of regeneration. Biochemistry. 32: 2680-9. PMID 8448124  0.6
1993 Rothwarf DM, Scheraga HA. Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution. Biochemistry. 32: 2671-9. PMID 8448123  0.6
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  0.48
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  0.48
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  1
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  1
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  1
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  1
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  1
1992 Rothwarf DM, Scheraga HA. Equilibrium and kinetic constants for the thiol-disulfide interchange reaction between glutathione and dithiothreitol. Proceedings of the National Academy of Sciences of the United States of America. 89: 7944-8. PMID 1518818  0.6
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  1
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  1
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  1
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  1
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  0.72
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  1
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  1
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  1
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  1
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  0.72
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  1
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  0.72
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  0.72
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  0.72
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  0.72
1987 Piela L, Némethy G, Scheraga HA. Proline-induced constraints in alpha-helices. Biopolymers. 26: 1587-600. PMID 3663874 DOI: 10.1002/bip.360260910  0.72
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  1
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  0.72
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  0.72
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  0.72
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  1
1986 Némethy G, Scheraga HA. Stabilization of collagen fibrils by hydroxyproline. Biochemistry. 25: 3184-8. PMID 3730354  0.72
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  1
1985 Chou KC, Némethy G, Rumsey S, Tuttle RW, Scheraga HA. Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins. Journal of Molecular Biology. 186: 591-609. PMID 4093981  0.72
1985 Chou KC, Némethy G, Pottle MS, Scheraga HA. Folding of the twisted beta-sheet in bovine pancreatic trypsin inhibitor. Biochemistry. 24: 7948-53. PMID 4092045  0.72
1985 Gerritsen M, Chou KC, Némethy G, Scheraga HA. Energetics of multihelix interactions in protein folding: application to myoglobin. Biopolymers. 24: 1271-91. PMID 4027345 DOI: 10.1002/bip.360240714  0.72
1985 Stimson ER, Huang SG, Némethy G, Leach SJ, Scheraga HA. Conformational analysis of cyclized dipeptide models for specific types of beta-bends by two-dimensional nuclear Overhauser spectroscopy. International Journal of Peptide and Protein Research. 25: 89-98. PMID 3980149  0.72
1984 Némethy G, Scheraga HA. Role of proline ... proline interactions in the packing of collagenlike poly(tripeptide) triple helices. Biopolymers. 23: 2781-99. PMID 6525401 DOI: 10.1002/bip.360231207  1
1984 Lee E, Némethy G, Scheraga HA, Ananthanarayanan VS. Beta-bend conformation of CH3CO-Pro-Pro-Gly-Pro-NHCH3: implications for posttranslational proline hydroxylation in collagen. Biopolymers. 23: 1193-206. PMID 6466764 DOI: 10.1002/bip.360230705  1
1984 Lin SH, Konishi Y, Denton ME, Scheraga HA. Influence of an extrinsic cross-link on the folding pathway of ribonuclease A. Conformational and thermodynamic analysis of cross-linked (lysine7-lysine41)-ribonuclease a. Biochemistry. 23: 5504-12. PMID 6210105  1
1984 Naik VM, Krimm S, Denton JB, Némethy G, Scheraga HA. Vibrational analysis of peptides, polypeptides and proteins. XXVII. Structure of gramicidin S from normal mode analyses of low-energy conformations. International Journal of Peptide and Protein Research. 24: 613-26. PMID 6085071  1
1981 Han SL, Stimson ER, Maxfield FR, Scheraga HA. Spectroscopic study of the conformations of proline-containing oligopeptides in the crystalline state and in solution. International Journal of Peptide and Protein Research. 17: 297-315. PMID 7287301  1
1981 Scheule RK, Han SL, Van Wart HE, Vallee BL, Scheraga HA. Resonance Raman spectroscopy of arsanilazocarboxypeptidase A: Mode of inhibitor binding and active-site topography Biochemistry. 20: 1778-1784. PMID 7225358  1
1980 Rackovsky S, Scheraga HA. Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S. Proceedings of the National Academy of Sciences of the United States of America. 77: 6965-7. PMID 16592928  1
1980 Han SL, Stimson ER, Maxfield FR, Leach SJ, Scheraga HA. Study of the state of ionization of [Leu5]-enkephalin in the crystal and in solution. International Journal of Peptide and Protein Research. 16: 183-90. PMID 7461900  1
1980 Han SL, Stimson ER, Maxfield FR, Scheraga HA. Conformational study of [Leu5]-enkephalin by laser Raman spectroscopy. International Journal of Peptide and Protein Research. 16: 173-81. PMID 7461899  1
1980 Isogai Y, Némethy G, Rackovsky S, Leach SJ, Scheraga HA. Characterization of multiple bends in proteins. Biopolymers. 19: 1183-210. PMID 7378550 DOI: 10.1002/bip.1980.360190607  1
1980 Scheule RK. Resonance raman spectroscopy of arsanilazocarboxypeptidase A: Conformational equilibria in solution and crystal phases Biochemistry. 19: 759-766. PMID 7356956  0.04
1979 Deslauriers R, Leach SJ, Maxfield FR, Minasian E, McQuie JR, Meinwald YC, Némethy G, Pottle MS, Rae ID, Scheraga HA, Stimson ER, Van Nispen JW. Cyclized dipeptide model for a beta-bend. Proceedings of the National Academy of Sciences of the United States of America. 76: 2512-4. PMID 288041 DOI: 10.1073/pnas.76.6.2512  1
1979 Maxfield FR, Scheraga HA. Improvements in the prediction of protein backbone topography by reduction of statistical errors. Biochemistry. 18: 697-704. PMID 217422  0.92
1978 Van Wart HE, Scheraga HA. Raman and resonance raman spectroscopy. Methods in Enzymology. 49: 67-149. PMID 651675  1
1978 Rackovsky S, Scheraga HA. Influence of ordered backbone structure on protein folding. A study of some simple models. Macromolecules. 11: 1-8. PMID 621950  1
1977 Maxfield FR, Scheraga HA. A Raman spectroscopic investigation of the disulfide conformation in oxytocin and lysine vasopressin. Biochemistry. 16: 4443-9. PMID 911768  0.92
1977 Matheson RR, Van Wart HE, Burgess AW, Weinstein LI, Scheraga HA. Study of protein topography with flash photolytically generated nonspecific surface-labeling reagents: surface labeling of ribonuclease A. Biochemistry. 16: 396-403. PMID 556946  1
1977 Rackovsky S, Scheraga HA. Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins. Proceedings of the National Academy of Sciences of the United States of America. 74: 5248-51. PMID 271950  1
1977 Van Wart HE, Scheraga HA. Stable conformations of aliphatic disulfides: influence of 1,4 interactions involving sulfur atoms. Proceedings of the National Academy of Sciences of the United States of America. 74: 13-7. PMID 264666  1
1977 Scheule RK, Van Wart HE, Vallee BL, Scheraga HA. Resonance Raman spectroscopy of arsanilazocarboxypeptidase A: determination of the nature of the azotyrosyl-248 zinc complex Proceedings of the National Academy of Sciences of the United States of America. 74: 3273-3277. PMID 20625  1
1976 Maxfield FR, Scheraga HA. Status of empirical methods for the prediction of protein backbone topography. Biochemistry. 15: 5138-53. PMID 990270  0.92
1975 Maxfield FR, Scheraga HA. The effect of neighboring charges on the helix forming ability of charged amino acids in proteins. Macromolecules. 8: 491-3. PMID 1177494  0.92
1975 Maxfield FR, Alter JE, Taylor GT, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. IX. Glutamic acid parameters from random poly(hydroxybutylglutamine-co-L-glutamic acid). Macromolecules. 8: 479-91. PMID 240987  1
1973 Van Wart HE, Lewis A, Scheraga HA, Saeva FD. Disulfide bond dihedral angles from Raman spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 70: 2619-23. PMID 16592108  1
1973 Van Wart HE, Taylor GT, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. VII. Phenylalanine parameters from random poly(hydroxypropylglutamine-co-L-phenylalanine). Macromolecules. 6: 266-73. PMID 4778413  1
1969 Ingwall JS, Scheraga HA. Purification and properties of bovine prothrombin. Biochemistry. 8: 1860-9. PMID 5814933  1
1966 Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Némethy G, Ramachandran GN, Scheraga HA. A proposal of standard conventions and nomenclature for the description of polypeptide conformations. Journal of Molecular Biology. 15: 399-407. PMID 5912052  1
1966 Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Nemethy G, Ramachandran GN, Scheraga HA. A proposal of standard conventions and nomenclature for the description of polypeptide conformation. The Journal of Biological Chemistry. 241: 1004-8. PMID 5905118  1
1965 Poland DC, Scheraga HA. Comparison of theories of the helix-coil transition in polypeptides. The Journal of Chemical Physics. 43: 2071-4. PMID 5845857  1
1964 WINZOR DJ, SCHERAGA HA. TITRATION BEHAVIOR OF BOVINE THROMBIN. Archives of Biochemistry and Biophysics. 104: 202-7. PMID 14163883  1
1963 WINZOR DJ, SCHERAGA HA. STUDIES OF CHEMICALLY REACTING SYSTEMS ON SEPHADEX. I. CHROMATOGRAPHIC DEMONSTRATION OF THE GILBERT THEORY. Biochemistry. 2: 1263-7. PMID 14093900  1
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