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Martin Karplus - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
electronic structure, geometry, and dynamics of molecules of chemical and biological interest
Website:
http://www.chem.harvard.edu/research/faculty/martin_karplus.php
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Year Citation  Score
2023 Salehi SM, Pezzella M, Willard A, Meuwly M, Karplus M. Water dynamics around T vs R of hemoglobin from local hydrophobicity analysis. The Journal of Chemical Physics. 158: 025101. PMID 36641390 DOI: 10.1063/5.0129990  0.789
2022 Conti S, Karplus M. A Computational Framework for Determining the Breadth of Antibodies Against Highly Mutable Pathogens. Methods in Molecular Biology (Clifton, N.J.). 2552: 399-408. PMID 36346605 DOI: 10.1007/978-1-0716-2609-2_22  0.684
2022 Conti S, Ovchinnikov V, Karplus M. ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning. Journal of Computational Chemistry. PMID 35930347 DOI: 10.1002/jcc.26974  0.726
2022 Conti S, Ovchinnikov V, Faris JG, Chakraborty AK, Karplus M, Sprenger KG. Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV. Plos Computational Biology. 18: e1009391. PMID 35442968 DOI: 10.1371/journal.pcbi.1009391  0.744
2022 Ovchinnikov V, Munasinghe A, Karplus M. Molecular Simulation of Stapled Peptides. Methods in Molecular Biology (Clifton, N.J.). 2405: 283-301. PMID 35298819 DOI: 10.1007/978-1-0716-1855-4_14  0.795
2021 Meuwly M, Karplus M. The functional role of the hemoglobin-water interface. Molecular Aspects of Medicine. 101042. PMID 34756740 DOI: 10.1016/j.mam.2021.101042  0.512
2021 Conti S, Kaczorowski KJ, Song G, Porter K, Andrabi R, Burton DR, Chakraborty AK, Karplus M. Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33637649 DOI: 10.1073/pnas.2018338118  0.729
2020 Ovchinnikov V, Conti S, Karplus M. A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems. The Journal of Chemical Physics. 153: 121103. PMID 33003727 DOI: 10.1063/5.0018026  0.73
2020 Pezzella M, El Hage K, Niesen M, Shin S, Willard AP, Meuwly M, Karplus M. Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin. The Journal of Physical Chemistry. B. PMID 32589026 DOI: 10.1021/Acs.Jpcb.0C04320  0.79
2020 Ovchinnikov V, Conti S, Lau EY, Lightstone FC, Karplus M. Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model. Journal of Chemical Theory and Computation. PMID 32045240 DOI: 10.1021/Acs.Jctc.9B01072  0.765
2019 Nam K, Karplus M. Insights into the origin of the high energy-conversion efficiency of F-ATPase. Proceedings of the National Academy of Sciences of the United States of America. PMID 31341091 DOI: 10.1073/Pnas.1906816116  0.303
2019 El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M. Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. Elife. 8. PMID 31219783 DOI: 10.7554/Elife.45318  0.785
2019 Conti S, Karplus M. Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning. Plos Computational Biology. 15: e1006954. PMID 30970017 DOI: 10.1371/Journal.Pcbi.1006954  0.719
2019 Hage KE, Hédin F, Gupta PK, Meuwly M, Karplus M. Author response: Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' Elife. DOI: 10.7554/Elife.45318.012  0.617
2018 Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD. Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Protein Science : a Publication of the Protein Society. PMID 30152054 DOI: 10.1002/Pro.3453  0.317
2018 Ovchinnikov V, Stone TA, Deber CM, Karplus M. Structure of the multidrug transporter and its use for inhibitor peptide design. Proceedings of the National Academy of Sciences of the United States of America. PMID 30082384 DOI: 10.1073/Pnas.1802177115  0.33
2018 El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M. Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size. Elife. 7. PMID 29998846 DOI: 10.7554/Elife.35560  0.797
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies. Elife. 7. PMID 29442996 DOI: 10.7554/Elife.33038  0.472
2018 Hage KE, Hédin F, Gupta PK, Meuwly M, Karplus M. Author response: Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size Elife. DOI: 10.7554/Elife.35560.024  0.626
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Author response: Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies Elife. DOI: 10.7554/Elife.33038.022  0.423
2017 Hwang W, Lang M, Karplus M. Kinesin motility driven by subdomain dynamics. Elife. 6. PMID 29111975 DOI: 10.7554/Elife.28948  0.345
2017 Meroz Y, Ovchinnikov V, Karplus M. Coexisting origins of subdiffusion in internal dynamics of proteins. Physical Review. E. 95: 062403. PMID 28709262 DOI: 10.1103/Physreve.95.062403  0.421
2016 Ovchinnikov V, Nam K, Karplus M. A Simple and Accurate Method to Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes. The Journal of Physical Chemistry. B. PMID 27135391 DOI: 10.1021/Acs.Jpcb.6B02139  0.375
2014 Nam K, Pu J, Karplus M. Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism. Proceedings of the National Academy of Sciences of the United States of America. 111: 17851-6. PMID 25453082 DOI: 10.1073/Pnas.1419486111  0.683
2014 Karplus M. Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel Lecture). Angewandte Chemie (International Ed. in English). 53: 9992-10005. PMID 25066036 DOI: 10.1002/Anie.201403924  0.329
2014 Ovchinnikov V, Karplus M. Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method. The Journal of Chemical Physics. 140: 175103. PMID 24811667 DOI: 10.1063/1.4871685  0.368
2014 Kalgin IV, Chekmarev SF, Karplus M. First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach? The Journal of Physical Chemistry. B. 118: 4287-99. PMID 24669953 DOI: 10.1021/Jp412729R  0.384
2014 Karplus M, Lavery R. Significance of Molecular Dynamics Simulations for Life Sciences Israel Journal of Chemistry. 54: 1042-1051. DOI: 10.1002/Ijch.201400074  0.343
2013 Zheng G, Schaefer M, Karplus M. Hemoglobin Bohr effects: atomic origin of the histidine residue contributions. Biochemistry. 52: 8539-55. PMID 24224786 DOI: 10.1021/Bi401126Z  0.594
2013 Calimet N, Simoes M, Changeux JP, Karplus M, Taly A, Cecchini M. A gating mechanism of pentameric ligand-gated ion channels. Proceedings of the National Academy of Sciences of the United States of America. 110: E3987-96. PMID 24043807 DOI: 10.1073/Pnas.1313785110  0.546
2013 Kalgin IV, Caflisch A, Chekmarev SF, Karplus M. New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry. B. 117: 6092-105. PMID 23621790 DOI: 10.1021/Jp401742Y  0.561
2013 Ovchinnikov V, Cecchini M, Karplus M. A simplified confinement method for calculating absolute free energies and free energy and entropy differences. The Journal of Physical Chemistry. B. 117: 750-62. PMID 23268557 DOI: 10.1021/Jp3080578  0.614
2013 Warshel A, Karplus M. Reprint of: Semiclassical trajectory approach to photoisomerization Chemical Physics Letters. 589: 68-72. DOI: 10.1016/J.Cplett.2013.10.028  0.52
2012 Karthikeyan G, Zambaldo C, Barluenga S, Zoete V, Karplus M, Winssinger N. Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 8978-86. PMID 22696415 DOI: 10.1002/Chem.201200546  0.528
2012 Ovchinnikov V, Karplus M. Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. The Journal of Physical Chemistry. B. 116: 8584-603. PMID 22409258 DOI: 10.1021/Jp212634Z  0.371
2011 Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M. A conformational transition in the myosin VI converter contributes to the variable step size. Biophysical Journal. 101: 2436-44. PMID 22098742 DOI: 10.1016/J.Bpj.2011.09.044  0.581
2011 Zheng G, Niklasson AM, Karplus M. Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method. The Journal of Chemical Physics. 135: 044122. PMID 21806105 DOI: 10.1063/1.3605303  0.6
2011 Karplus M. Behind the folding funnel diagram. Nature Chemical Biology. 7: 401-4. PMID 21685880 DOI: 10.1038/Nchembio.565  0.354
2011 Luo G, Karplus M. Determining the conformational change that accompanies donor-acceptor distance fluctuations: an umbrella sampling analysis. The Journal of Physical Chemistry. B. 115: 7991-5. PMID 21619043 DOI: 10.1021/Jp201998C  0.349
2011 Fischer S, Olsen KW, Nam K, Karplus M. Unsuspected pathway of the allosteric transition in hemoglobin. Proceedings of the National Academy of Sciences of the United States of America. 108: 5608-13. PMID 21415366 DOI: 10.1073/Pnas.1011995108  0.563
2011 Ovchinnikov V, Karplus M, Vanden-Eijnden E. Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. The Journal of Chemical Physics. 134: 085103. PMID 21361558 DOI: 10.1063/1.3544209  0.367
2010 Rao F, Karplus M. Protein dynamics investigated by inherent structure analysis. Proceedings of the National Academy of Sciences of the United States of America. 107: 9152-7. PMID 20435910 DOI: 10.1073/Pnas.0915087107  0.416
2010 Karplus M. Role of conformation transitions in adenylate kinase. Proceedings of the National Academy of Sciences of the United States of America. 107: E71; author reply E7. PMID 20424124 DOI: 10.1073/Pnas.1002180107  0.308
2010 Cecchini M, Alexeev Y, Karplus M. Pi release from myosin: a simulation analysis of possible pathways. Structure (London, England : 1993). 18: 458-70. PMID 20399183 DOI: 10.1016/J.Str.2010.01.014  0.572
2010 Karplus M. Dynamical aspects of molecular recognition. Journal of Molecular Recognition : Jmr. 23: 102-4. PMID 20151415 DOI: 10.1002/Jmr.1018  0.31
2010 Grinthal A, Adamovic I, Weiner B, Karplus M, Kleckner N. PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis. Proceedings of the National Academy of Sciences of the United States of America. 107: 2467-72. PMID 20133745 DOI: 10.1073/Pnas.0914073107  0.348
2010 Ovchinnikov V, Trout BL, Karplus M. Mechanical coupling in myosin V: a simulation study. Journal of Molecular Biology. 395: 815-33. PMID 19853615 DOI: 10.1016/J.Jmb.2009.10.029  0.342
2010 Levy RM, Perahia D, Karplus M. Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proceedings of the National Academy of Sciences of the United States of America. 79: 1346-50. PMID 16593164 DOI: 10.1073/Pnas.79.4.1346  0.662
2010 Spichty M, Cecchini M, Karplus M. Conformational free-energy difference of a miniprotein from nonequilibrium simulations Journal of Physical Chemistry Letters. 1: 1922-1926. DOI: 10.1021/Jz1005016  0.639
2010 Hwang W, Lang MJ, Karplus M. Free Energy Changes During Kinesin's Force-Generating Substep Biophysical Journal. 98: 369a. DOI: 10.1016/J.Bpj.2009.12.1993  0.344
2010 Karplus M, Pu J. How biomolecular motors work: Synergy between single molecule experiments and single molecule simulations Springer Series in Chemical Physics. 96: 3-22. DOI: 10.1007/978-3-642-02597-6_1  0.626
2010 Simonson T, Archontis G, Karplus M. ChemInform Abstract: Free Energy Simulations Come of Age: Protein-Ligand Recognition Cheminform. 33: no-no. DOI: 10.1002/chin.200237290  0.655
2010 DOBSON CM, SALI A, KARPLUS M. ChemInform Abstract: Protein Folding: A Perspective from Theory and Experiment Cheminform. 29: no-no. DOI: 10.1002/chin.199826366  0.339
2010 Grootenhuis PDJ, van Geerestein VJ, Haasnoot CAG, Karplus M. Molecular Modelling of Protein - Ligand Interactions Bulletin Des SociéTéS Chimiques Belges. 101: 661-662. DOI: 10.1002/Bscb.19921010713  0.312
2009 Nam K, Verdine GL, Karplus M. Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism. Journal of the American Chemical Society. 131: 18208-9. PMID 19961158 DOI: 10.1021/Ja907544B  0.33
2009 Kalgin IV, Karplus M, Chekmarev SF. Folding of a SH3 domain: standard and "hydrodynamic" analyses. The Journal of Physical Chemistry. B. 113: 12759-72. PMID 19711956 DOI: 10.1021/Jp903325Z  0.364
2009 Lei M, Velos J, Gardino A, Kivenson A, Karplus M, Kern D. Segmented transition pathway of the signaling protein nitrogen regulatory protein C. Journal of Molecular Biology. 392: 823-36. PMID 19576227 DOI: 10.1016/J.Jmb.2009.06.065  0.397
2009 Cecchini M, Krivov SV, Spichty M, Karplus M. Calculation of free-energy differences by confinement simulations. Application to peptide conformers. The Journal of Physical Chemistry. B. 113: 9728-40. PMID 19552392 DOI: 10.1021/Jp9020646  0.644
2009 Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M. The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts. Biophysical Chemistry. 143: 111-23. PMID 19482409 DOI: 10.1016/J.Bpc.2009.04.003  0.571
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, ... ... Karplus M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.789
2009 Maragakis P, van der Vaart A, Karplus M. Gaussian-mixture umbrella sampling. The Journal of Physical Chemistry. B. 113: 4664-73. PMID 19284746 DOI: 10.1021/Jp808381S  0.633
2009 Kong Y, Karplus M. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins. 74: 145-54. PMID 18618698 DOI: 10.1002/Prot.22139  0.329
2009 Lei M, Velos J, Gardino A, Karplus M, Kern D. Segmented Transition Pathway Of The Receiver Domain Of Nitrogen Regulatory Protein C Biophysical Journal. 96: 586a. DOI: 10.1016/J.Bpj.2008.12.3069  0.335
2009 Grinthal AE, Adamovic I, Karplus M, Kleckner N. The Scaffolding Subunit of PP2A is a Coherent Linear Elastic Object That Can Transmit Mechanical Information Along Its Length Biophysical Journal. 96: 70a. DOI: 10.1016/J.Bpj.2008.12.262  0.314
2009 Nam K, Verdine GL, Karplus M. Molecular Mechanism of the Acceleration of the Damaged Base Extrusion and its Recognition by Bacterial MutM DNA Glycosylase: Free Energy Simulation Studies Biophysical Journal. 96: 342a. DOI: 10.1016/J.Bpj.2008.12.1716  0.309
2008 Khalil AS, Appleyard DC, Labno AK, Georges A, Karplus M, Belcher AM, Hwang W, Lang MJ. Kinesin's cover-neck bundle folds forward to generate force. Proceedings of the National Academy of Sciences of the United States of America. 105: 19247-52. PMID 19047639 DOI: 10.1073/Pnas.0805147105  0.306
2008 Krivov SV, Karplus M. Diffusive reaction dynamics on invariant free energy profiles. Proceedings of the National Academy of Sciences of the United States of America. 105: 13841-6. PMID 18772379 DOI: 10.1073/Pnas.0800228105  0.326
2008 Cecchini M, Houdusse A, Karplus M. Allosteric communication in myosin V: from small conformational changes to large directed movements. Plos Computational Biology. 4: e1000129. PMID 18704171 DOI: 10.1371/Journal.Pcbi.1000129  0.568
2008 Maragakis P, Ritort F, Bustamante C, Karplus M, Crooks GE. Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. The Journal of Chemical Physics. 129: 024102. PMID 18624511 DOI: 10.1063/1.2937892  0.301
2008 Krivov SV, Muff S, Caflisch A, Karplus M. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. The Journal of Physical Chemistry. B. 112: 8701-14. PMID 18590307 DOI: 10.1021/Jp711864R  0.568
2008 Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science : a Publication of the Protein Society. 17: 1295-307. PMID 18560010 DOI: 10.1110/Ps.03259908  0.569
2008 Maragakis P, Spichty M, Karplus M. A differential fluctuation theorem. The Journal of Physical Chemistry. B. 112: 6168-74. PMID 18331019 DOI: 10.1021/Jp077037R  0.382
2008 Adamovic I, Mijailovich SM, Karplus M. The elastic properties of the structurally characterized myosin II S2 subdomain: a molecular dynamics and normal mode analysis. Biophysical Journal. 94: 3779-89. PMID 18234833 DOI: 10.1529/Biophysj.107.122028  0.357
2008 Chekmarev SF, Palyanov AY, Karplus M. Hydrodynamic description of protein folding. Physical Review Letters. 100: 018107. PMID 18232827 DOI: 10.1103/Physrevlett.100.018107  0.324
2008 Pu J, Karplus M. How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 105: 1192-7. PMID 18216260 DOI: 10.1073/Pnas.0708746105  0.66
2008 Karplus M, Aminathan SSW, Ichiye T, Van Gunsteren WF. Local and Collective Motions in Protein Dynamics Ciba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids. 271-290. DOI: 10.1002/9780470720752.ch15  0.415
2007 Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature. 450: 913-6. PMID 18026087 DOI: 10.1038/Nature06407  0.376
2007 Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG, Kern D. Intrinsic motions along an enzymatic reaction trajectory. Nature. 450: 838-44. PMID 18026086 DOI: 10.1038/Nature06410  0.521
2007 Auer S, Miller MA, Krivov SV, Dobson CM, Karplus M, Vendruscolo M. Importance of metastable states in the free energy landscapes of polypeptide chains. Physical Review Letters. 99: 178104. PMID 17995375 DOI: 10.1103/Physrevlett.99.178104  0.612
2007 Evensen E, Joseph-McCarthy D, Weiss GA, Schreiber SL, Karplus M. Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. Journal of Computer-Aided Molecular Design. 21: 395-418. PMID 17657565 DOI: 10.1007/S10822-007-9119-X  0.722
2007 Kong Y, Karplus M. The signaling pathway of rhodopsin. Structure (London, England : 1993). 15: 611-23. PMID 17502106 DOI: 10.1016/J.Str.2007.04.002  0.342
2007 Wu Y, Gao YQ, Karplus M. A kinetic model of coordinated myosin V. Biochemistry. 46: 6318-30. PMID 17487986 DOI: 10.1021/Bi700526R  0.474
2007 van der Vaart A, Karplus M. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations. The Journal of Chemical Physics. 126: 164106. PMID 17477588 DOI: 10.1063/1.2719697  0.662
2007 Palyanov AY, Krivov SV, Karplus M, Chekmarev SF. A lattice protein with an amyloidogenic latent state: stability and folding kinetics. The Journal of Physical Chemistry. B. 111: 2675-87. PMID 17315918 DOI: 10.1021/Jp067027A  0.375
2007 Golosov AA, Karplus M. Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis. The Journal of Physical Chemistry. B. 111: 1482-90. PMID 17249715 DOI: 10.1021/Jp065493U  0.394
2006 Ma A, Hu J, Karplus M, Dinner AR. Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved. Biochemistry. 45: 13687-96. PMID 17105188 DOI: 10.1021/Bi061061Y  0.693
2006 Krivov SV, Karplus M. One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers. The Journal of Physical Chemistry. B. 110: 12689-98. PMID 16800603 DOI: 10.1021/Jp060039B  0.36
2006 Lopez X, Dejaegere A, Leclerc F, York DM, Karplus M. Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. The Journal of Physical Chemistry. B. 110: 11525-39. PMID 16771429 DOI: 10.1021/Jp0603942  0.78
2006 Bitetti-Putzer R, Dinner AR, Yang W, Karplus M. Conformational sampling via a self-regulating effective energy surface. The Journal of Chemical Physics. 124: 174901. PMID 16689598 DOI: 10.1063/1.2171194  0.571
2006 Luo G, Andricioaei I, Xie XS, Karplus M. Dynamic distance disorder in proteins is caused by trapping. The Journal of Physical Chemistry. B. 110: 9363-7. PMID 16686476 DOI: 10.1021/Jp057497P  0.751
2006 Levinson NM, Kuchment O, Shen K, Young MA, Koldobskiy M, Karplus M, Cole PA, Kuriyan J. A Src-like inactive conformation in the abl tyrosine kinase domain. Plos Biology. 4: e144. PMID 16640460 DOI: 10.1371/Journal.Pbio.0040144  0.784
2006 Chekmarev SF, Krivov SV, Karplus M. Folding of ubiquitin: a simple model describes the strange kinetics. The Journal of Physical Chemistry. B. 110: 8865-9. PMID 16640446 DOI: 10.1021/Jp056799O  0.302
2006 Maragakis P, Spichty M, Karplus M. Optimal estimates of free energies from multistate nonequilibrium work data. Physical Review Letters. 96: 100602. PMID 16605720 DOI: 10.1103/Physrevlett.96.100602  0.331
2006 Kong Y, Ma J, Karplus M, Lipscomb WN. The allosteric mechanism of yeast chorismate mutase: a dynamic analysis. Journal of Molecular Biology. 356: 237-47. PMID 16337651 DOI: 10.1016/J.Jmb.2005.10.064  0.513
2006 Pal'yanov AY, Titov II, Chekmarev SF, Karplus M. Simulation of protein misfolding using a lattice model Biophysics. 51: 44-48. DOI: 10.1134/S0006350906070098  0.387
2006 Gao YQ, Yang W, Karplus M. Thermodynamics and kinetic analysis of F0F1-ATPase Modern Methods For Theoretical Physical Chemistry of Biopolymers. 249-263. DOI: 10.1016/B978-044452220-7/50077-0  0.388
2006 Zhou Y, Zhou H, Karplus M. Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water Rendiconti Lincei. 17: 192-211. DOI: 10.1007/BF02904509  0.477
2005 Chekmarev SF, Krivov SV, Karplus M. Folding time distributions as an approach to protein folding kinetics. The Journal of Physical Chemistry. B. 109: 5312-30. PMID 16863198 DOI: 10.1021/Jp047012H  0.363
2005 Nutt DR, Karplus M, Meuwly M. Potential energy surface and molecular dynamics of MbNO: existence of an unsuspected FeON minimum. The Journal of Physical Chemistry. B. 109: 21118-25. PMID 16853735 DOI: 10.1021/Jp0523975  0.637
2005 Archontis G, Watson KA, Xie Q, Andreou G, Chrysina ED, Zographos SE, Oikonomakos NG, Karplus M. Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues. Proteins. 61: 984-98. PMID 16245298 DOI: 10.1002/Prot.20641  0.695
2005 Gao YQ, Yang W, Karplus M. A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell. 123: 195-205. PMID 16239139 DOI: 10.1016/J.Cell.2005.10.001  0.449
2005 Maragakis P, Karplus M. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. Journal of Molecular Biology. 352: 807-22. PMID 16139299 DOI: 10.1016/J.Jmb.2005.07.031  0.375
2005 Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M. Transition state contact orders correlate with protein folding rates. Journal of Molecular Biology. 352: 495-500. PMID 16120445 DOI: 10.1016/J.Jmb.2005.06.081  0.595
2005 Zoete V, Meuwly M, Karplus M. Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins. 61: 79-93. PMID 16080143 DOI: 10.1002/Prot.20528  0.557
2005 van Vlijmen HW, Karplus M. Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry. Journal of Molecular Biology. 350: 528-42. PMID 15922356 DOI: 10.1016/J.Jmb.2005.03.028  0.654
2005 Moulin E, Zoete V, Barluenga S, Karplus M, Winssinger N. Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues. Journal of the American Chemical Society. 127: 6999-7004. PMID 15884943 DOI: 10.1021/Ja043101W  0.577
2005 Best RB, Clarke J, Karplus M. What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. Journal of Molecular Biology. 349: 185-203. PMID 15876377 DOI: 10.1016/J.Jmb.2005.03.001  0.63
2005 Karplus M, Kuriyan J. Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America. 102: 6679-85. PMID 15870208 DOI: 10.1073/Pnas.0408930102  0.601
2005 van der Vaart A, Karplus M. Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. The Journal of Chemical Physics. 122: 114903. PMID 15836253 DOI: 10.1063/1.1861885  0.668
2005 Petrella RJ, Karplus M. Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation. Journal of Computational Chemistry. 26: 755-87. PMID 15800892 DOI: 10.1002/Jcc.20197  0.354
2005 Seeliger MA, Spichty M, Kelly SE, Bycroft M, Freund SM, Karplus M, Itzhaki LS. Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins. The Journal of Biological Chemistry. 280: 30448-59. PMID 15772084 DOI: 10.1074/Jbc.M501450200  0.67
2005 Vendruscolo M, Dobson CM, Zewail AH, Mcmillan PF, Davies JF, Karplus M, Simons JP. Towards complete descriptions of the free-energy landscapes of proteins Philosophical Transactions of the Royal Society a: Mathematical, Physical and Engineering Sciences. 363: 433-452. PMID 15664892 DOI: 10.1098/Rsta.2004.1501  0.597
2005 Sobott F, Mccammon MG, Hernández H, Robinson CV, Karplus M, Dobson CM, Scoles G, Zewail AH, McMillan PF, Finney JL. The flight of macromolecular complexes in a mass spectrometer Philosophical Transactions of the Royal Society a: Mathematical, Physical and Engineering Sciences. 363: 379-391. PMID 15664889 DOI: 10.1098/rsta.2004.1498  0.498
2005 Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496  0.679
2004 Wan S, Stote RH, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. The Journal of Chemical Physics. 121: 9539-48. PMID 15538876 DOI: 10.1063/1.1789935  0.685
2004 Krivov SV, Karplus M. Hidden complexity of free energy surfaces for peptide (protein) folding. Proceedings of the National Academy of Sciences of the United States of America. 101: 14766-70. PMID 15466711 DOI: 10.1073/Pnas.0406234101  0.336
2004 Islam SA, Karplus M, Weaver DL. The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G. Structure (London, England : 1993). 12: 1833-45. PMID 15458632 DOI: 10.1016/J.Str.2004.06.024  0.594
2004 Andricioaei I, Goel A, Herschbach D, Karplus M. Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations. Biophysical Journal. 87: 1478-97. PMID 15345530 DOI: 10.1529/Biophysj.103.039313  0.772
2004 Zoete V, Meuwly M, Karplus M. A comparison of the dynamic behavior of monomeric and dimeric insulin shows structural rearrangements in the active monomer. Journal of Molecular Biology. 342: 913-29. PMID 15342246 DOI: 10.1016/J.Jmb.2004.07.033  0.526
2004 Hwang W, Zhang S, Kamm RD, Karplus M. Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proceedings of the National Academy of Sciences of the United States of America. 101: 12916-21. PMID 15326301 DOI: 10.1073/Pnas.0402634101  0.341
2004 Ruiz F, Hazemann I, Mitschler A, Joachimiak A, Schneider T, Karplus M, Podjarny A. The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48. Acta Crystallographica. Section D, Biological Crystallography. 60: 1347-54. PMID 15272156 DOI: 10.1107/S0907444904011370  0.331
2004 Yang W, Bitetti-Putzer R, Karplus M. Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. The Journal of Chemical Physics. 120: 2618-28. PMID 15268405 DOI: 10.1063/1.1638996  0.353
2004 Yang W, Bitetti-Putzer R, Karplus M. Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials. The Journal of Chemical Physics. 120: 9450-3. PMID 15267955 DOI: 10.1063/1.1738106  0.351
2004 van der Vaart A, Ma J, Karplus M. The unfolding action of GroEL on a protein substrate. Biophysical Journal. 87: 562-73. PMID 15240489 DOI: 10.1529/Biophysj.103.037333  0.653
2004 Best RB, Clarke J, Karplus M. The origin of protein sidechain order parameter distributions. Journal of the American Chemical Society. 126: 7734-5. PMID 15212494 DOI: 10.1021/Ja049078W  0.594
2004 Cui Q, Li G, Ma J, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. Journal of Molecular Biology. 340: 345-72. PMID 15201057 DOI: 10.1016/J.Jmb.2004.04.044  0.551
2004 Mattos C, Cohen JD, Green DF, Tidor B, Karplus M. X-ray structural and simulation analysis of a protein mutant: the value of a combined approach. Proteins. 55: 733-42. PMID 15103635 DOI: 10.1002/Prot.20031  0.806
2004 Zoete V, Meuwly M, Karplus M. Investigation of glucose binding sites on insulin. Proteins. 55: 568-81. PMID 15103621 DOI: 10.1002/Prot.20071  0.538
2004 Karplus M, Gao YQ. Biomolecular motors: the F1-ATPase paradigm. Current Opinion in Structural Biology. 14: 250-9. PMID 15093841 DOI: 10.1016/J.Sbi.2004.03.012  0.444
2004 Meuwly M, Karplus M. Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron transfer on protein dynamics. Biophysical Journal. 86: 1987-2007. PMID 15041642 DOI: 10.1016/S0006-3495(04)74261-7  0.543
2004 Petrella RJ, Karplus M. The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations. Proteins. 54: 716-26. PMID 14997567 DOI: 10.1002/Prot.10577  0.325
2004 Paci E, Friel CT, Lindorff-Larsen K, Radford SE, Karplus M, Vendruscolo M. Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. Proteins. 54: 513-25. PMID 14747999 DOI: 10.1002/Prot.10595  0.534
2004 Garcia-Viloca M, Gao J, Karplus M, Truhlar DG. How enzymes work: analysis by modern rate theory and computer simulations. Science (New York, N.Y.). 303: 186-95. PMID 14716003 DOI: 10.1126/Science.1088172  0.676
2004 Lagant P, Nolde D, Stote R, Vergoten G, Karplus M. Increasing normal modes analysis accuracy: The SPASIBA spectroscopic force field introduced into the CHARMM program Journal of Physical Chemistry A. 108: 4019-4029. DOI: 10.1021/Jp031178L  0.659
2003 Zoete V, Michielin O, Karplus M. Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. Journal of Computer-Aided Molecular Design. 17: 861-80. PMID 15124934 DOI: 10.1023/B:Jcam.0000021882.99270.4C  0.37
2003 Vendruscolo M, Paci E, Dobson CM, Karplus M. Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. Journal of the American Chemical Society. 125: 15686-7. PMID 14677926 DOI: 10.1021/Ja036523Z  0.592
2003 Vendruscolo M, Paci E, Karplus M, Dobson CM. Structures and relative free energies of partially folded states of proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 14817-21. PMID 14657374 DOI: 10.1073/Pnas.2036516100  0.62
2003 Cui Q, Karplus M. Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase. Advances in Protein Chemistry. 66: 315-72. PMID 14631822 DOI: 10.1016/S0065-3233(03)66008-0  0.565
2003 Meuwly M, Karplus M. Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on the coupled electron proton transfer reaction. Faraday Discussions. 124: 297-313; discussion . PMID 14527222 DOI: 10.1039/B211407K  0.529
2003 Gao YQ, Yang W, Marcus RA, Karplus M. A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 11339-44. PMID 14500780 DOI: 10.1073/Pnas.1334188100  0.61
2003 Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angewandte Chemie (International Ed. in English). 42: 1508-11. PMID 12698486 DOI: 10.1002/Anie.200219878  0.708
2003 Lazaridis T, Karplus M. Thermodynamics of protein folding: a microscopic view. Biophysical Chemistry. 100: 367-95. PMID 12646378 DOI: 10.1016/S0301-4622(02)00293-4  0.657
2003 Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. Journal of Computational Chemistry. 24: 565-81. PMID 12632471 DOI: 10.1002/Jcc.10201  0.599
2003 Reddy SY, Leclerc F, Karplus M. DNA polymorphism: a comparison of force fields for nucleic acids. Biophysical Journal. 84: 1421-49. PMID 12609851 DOI: 10.1016/S0006-3495(03)74957-1  0.315
2003 Karplus M. Molecular dynamics of biological macromolecules: a brief history and perspective. Biopolymers. 68: 350-8. PMID 12601794 DOI: 10.1002/Bip.10266  0.326
2003 Zhou Y, Zhou H, Karplus M. Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water. Journal of Molecular Biology. 326: 593-606. PMID 12559925 DOI: 10.1016/S0022-2836(02)01329-3  0.568
2003 Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 874-9. PMID 12552084 DOI: 10.1073/Pnas.0337432100  0.639
2003 Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M. Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proceedings of the National Academy of Sciences of the United States of America. 100: 394-9. PMID 12515856 DOI: 10.1073/Pnas.232704999  0.529
2003 Petrella RJ, Andricioaei I, Brooks BR, Karplus M. An improved method for nonbonded list generation: rapid determination of near-neighbor pairs. Journal of Computational Chemistry. 24: 222-31. PMID 12497601 DOI: 10.1002/Jcc.10123  0.773
2003 Andricioaei I, Dinner AR, Karplus M. Self-guided enhanced sampling methods for thermodynamic averages Journal of Chemical Physics. 118: 1074-1084. DOI: 10.1063/1.1528893  0.788
2003 Cui Q, Karplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase Journal of Physical Chemistry B. 107: 1071-1078. DOI: 10.1021/Jp021931V  0.589
2003 Boresch S, Tettinger F, Leitgeb M, Karplus M. Absolute binding free energies: A quantitative approach for their calculation Journal of Physical Chemistry B. 107: 9535-9551. DOI: 10.1021/Jp0217839  0.686
2003 Bitetti-Putzer R, Yang W, Karplus M. Generalized ensembles serve to improve the convergence of free energy simulations Chemical Physics Letters. 377: 633-641. DOI: 10.1016/S0009-2614(03)01057-1  0.367
2003 Dinner AR, Lopez X, Karplus M. A charge-scaling method to treat solvent in QM/MM simulations Theoretical Chemistry Accounts. 109: 118-124. DOI: 10.1007/S00214-002-0417-Z  0.596
2002 Paci E, Vendruscolo M, Karplus M. Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition. Biophysical Journal. 83: 3032-8. PMID 12496075 DOI: 10.1016/S0006-3495(02)75308-3  0.544
2002 Michielin O, Karplus M. Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. Journal of Molecular Biology. 324: 547-69. PMID 12445788 DOI: 10.1016/S0022-2836(02)00880-X  0.327
2002 Paci E, Vendruscolo M, Dobson CM, Karplus M. Determination of a transition state at atomic resolution from protein engineering data. Journal of Molecular Biology. 324: 151-63. PMID 12421565 DOI: 10.1016/S0022-2836(02)00944-0  0.63
2002 Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J. Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. Journal of Molecular Biology. 322: 841-9. PMID 12270718 DOI: 10.1016/S0022-2836(02)00805-7  0.621
2002 Michielin O, Zoete V, Gierasch TM, Eckstein J, Napper A, Verdine G, Karplus M. Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues. Journal of the American Chemical Society. 124: 11131-41. PMID 12224961 DOI: 10.1021/Ja012695P  0.308
2002 Sirockin F, Sich C, Improta S, Schaefer M, Saudek V, Froloff N, Karplus M, Dejaegere A. Structure activity relationship by NMR and by computer: a comparative study. Journal of the American Chemical Society. 124: 11073-84. PMID 12224955 DOI: 10.1021/Ja0265658  0.642
2002 Dutzler R, Schirmer T, Karplus M, Fischer S. Translocation mechanism of long sugar chains across the maltoporin membrane channel. Structure (London, England : 1993). 10: 1273-84. PMID 12220498 DOI: 10.1016/S0969-2126(02)00811-0  0.557
2002 Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nature Structural Biology. 9: 646-52. PMID 12198485 DOI: 10.1038/Nsb0902-646  0.529
2002 Vendruscolo M, Dokholyan NV, Paci E, Karplus M. Small-world view of the amino acids that play a key role in protein folding. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 061910. PMID 12188762 DOI: 10.1103/Physreve.65.061910  0.493
2002 Meuwly M, Becker OM, Stote R, Karplus M. NO rebinding to myoglobin: a reactive molecular dynamics study. Biophysical Chemistry. 98: 183-207. PMID 12128198 DOI: 10.1016/S0301-4622(02)00093-5  0.757
2002 Ma J, Flynn TC, Cui Q, Leslie AG, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure (London, England : 1993). 10: 921-31. PMID 12121647 DOI: 10.1016/S0969-2126(02)00789-X  0.584
2002 Simonson T, Archontis G, Karplus M. Free energy simulations come of age: protein-ligand recognition. Accounts of Chemical Research. 35: 430-7. PMID 12069628 DOI: 10.1021/Ar010030M  0.712
2002 Karplus M. Molecular dynamics simulations of biomolecules. Accounts of Chemical Research. 35: 321-3. PMID 12069615 DOI: 10.1021/Ar020082R  0.345
2002 Islam SA, Karplus M, Weaver DL. Application of the diffusion-collision model to the folding of three-helix bundle proteins. Journal of Molecular Biology. 318: 199-215. PMID 12054779 DOI: 10.1016/S0022-2836(02)00029-3  0.613
2002 Lopez X, Schaefer M, Dejaegere A, Karplus M. Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis. Journal of the American Chemical Society. 124: 5010-8. PMID 11982365 DOI: 10.1021/Ja011373I  0.667
2002 Paci E, Vendruscolo M, Karplus M. Native and non-native interactions along protein folding and unfolding pathways Proteins: Structure, Function and Genetics. 47: 379-392. PMID 11948791 DOI: 10.1002/Prot.10089  0.548
2002 Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. Journal of the American Chemical Society. 124: 3093-124. PMID 11902900 DOI: 10.1021/Ja0118439  0.603
2002 Vitkup D, Ringe D, Karplus M, Petsko GA. Why protein R-factors are so large: a self-consistent analysis. Proteins. 46: 345-54. PMID 11835510 DOI: 10.1002/Prot.10035  0.766
2002 Krivov SV, Chekmarev SF, Karplus M. Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide. Physical Review Letters. 88: 038101. PMID 11801090 DOI: 10.1103/Physrevlett.88.038101  0.349
2002 Zoete V, Michielin O, Karplus M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein Flexibility Journal of Molecular Biology. 315: 21-52. PMID 11771964 DOI: 10.1006/Jmbi.2001.5173  0.353
2002 Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods Journal of Chemical Physics. 117: 5617-5631. DOI: 10.1063/1.1501134  0.651
2002 Meuwly M, Karplus M. Simulation of proton transfer along ammonia wires: An "ab initio" and semiempirical density functional comparison of potentials and classical molecular dynamics Journal of Chemical Physics. 116: 2572-2585. DOI: 10.1063/1.1431285  0.558
2002 Zhou Y, Karplus M, Ball KD, Berry RS. The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers Journal of Chemical Physics. 116: 2323-2329. DOI: 10.1063/1.1426419  0.507
2002 Cui Q, Karplus M. Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems Journal of Physical Chemistry B. 106: 7927-7947. DOI: 10.1021/Jp0205057  0.571
2002 Cui Q, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH) Journal of Physical Chemistry B. 106: 2721-2740. DOI: 10.1021/Jp013012V  0.568
2002 Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: Verification of methodology and analysis of reaction mechanisms Journal of Physical Chemistry B. 106: 1768-1798. DOI: 10.1021/Jp012659C  0.323
2002 Dinner AR, So SS, Karplus M. Statistical analysis of protein folding kinetics Advances in Chemical Physics. 120: 1-34.  0.52
2001 Dinner AR, Karplus M. Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State" by van Gunsteren et al. We thank Eugene Shakhnovich (Harvard University) for pointing out the references on lattice polymer simulations and very helpful discussions. We also thank Wilfred van Gunsteren for comments on the manuscript. A.R.D. is a Burroughs Wellcome Fund Hitchings-Elion Postdoctoral Fellow. The work done at Harvard was supported in part by the National Institutes of Health. Angewandte Chemie (International Ed. in English). 40: 4615-4616. PMID 12404364 DOI: 10.1002/1521-3773(20011217)40:24<4615::Aid-Anie4615>3.0.Co;2-H  0.547
2001 Schaefer M, Bartels C, Leclerc F, Karplus M. Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. Journal of Computational Chemistry. 22: 1857-1879. PMID 12116417 DOI: 10.1002/Jcc.1137  0.307
2001 Bitetti-Putzer R, Joseph-McCarthy D, Hogle JM, Karplus M. Functional group placement in protein binding sites: a comparison of GRID and MCSS. Journal of Computer-Aided Molecular Design. 15: 935-60. PMID 11918077 DOI: 10.1023/A:1014309222984  0.325
2001 Paci E, Caflisch A, Plückthun A, Karplus M. Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study Journal of Molecular Biology. 314: 589-605. PMID 11846569 DOI: 10.1006/Jmbi.2001.5103  0.56
2001 Dinner AR, Blackburn GM, Karplus M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature. 413: 752-5. PMID 11607036 DOI: 10.1038/35099587  0.557
2001 Petrella RJ, Karplus M. The energetics of off-rotamer protein side-chain conformations. Journal of Molecular Biology. 312: 1161-75. PMID 11580256 DOI: 10.1006/Jmbi.2001.4965  0.383
2001 Guo H, Cui Q, Lipscomb WN, Karplus M. Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism. Proceedings of the National Academy of Sciences of the United States of America. 98: 9032-7. PMID 11481470 DOI: 10.1073/Pnas.141230998  0.723
2001 Cui Q, Karplus M. Triosephosphate isomerase: a theoretical comparison of alternative pathways. Journal of the American Chemical Society. 123: 2284-90. PMID 11456876 DOI: 10.1021/Ja002886C  0.59
2001 Paci E, Smith LJ, Dobson CM, Karplus M. Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation. Journal of Molecular Biology. 306: 329-47. PMID 11237603 DOI: 10.1006/Jmbi.2000.4337  0.491
2001 Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Journal of Molecular Biology. 306: 307-27. PMID 11237602 DOI: 10.1006/Jmbi.2000.4285  0.707
2001 Vendruscolo M, Paci E, Dobson CM, Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature. 409: 641-5. PMID 11214326 DOI: 10.1038/35054591  0.602
2001 Dinner AR, Karplus M. The roles of stability and contact order in determining protein folding rates. Nature Structural Biology. 8: 21-2. PMID 11135664 DOI: 10.1038/83003  0.557
2001 Zhou Y, Cook M, Karplus M. Protein motions at zero-total angular momentum: the importance of long-range correlations. Biophysical Journal. 79: 2902-8. PMID 11106598 DOI: 10.1016/S0006-3495(00)76527-1  0.555
2001 Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations Journal of Chemical Physics. 115: 6289-6292. DOI: 10.1063/1.1401821  0.719
2001 Buck M, Karplus M. Hydrogen Bond Energetics:  A Simulation and Statistical Analysis ofN-Methyl Acetamide (NMA), Water, and Human Lysozyme† The Journal of Physical Chemistry B. 105: 11000-11015. DOI: 10.1021/Jp011042S  0.34
2001 Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method The Journal of Physical Chemistry B. 105: 569-585. DOI: 10.1021/Jp0029109  0.596
2001 Schuman M, Lopez X, Karplus M, Gouverneur V. Synthesis of a novel diarylphosphinic acid: A distorted ground state mimic and transition state analogue for amide hydrolysis Tetrahedron. 57: 10299-10307. DOI: 10.1016/S0040-4020(01)01048-1  0.304
2001 Andricioaei I, Straub JE, Karplus M. Simulation of quantum systems using path integrals in a generalized ensemble Chemical Physics Letters. 346: 274-282. DOI: 10.1016/S0009-2614(01)00965-4  0.784
2001 Lopez X, York DM, Dejaegere A, Karplus M. Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A International Journal of Quantum Chemistry. 86: 10-26. DOI: 10.1002/Qua.1601  0.785
2000 Ma J, Sigler PB, Xu Z, Karplus M. A dynamic model for the allosteric mechanism of GroEL. Journal of Molecular Biology. 302: 303-13. PMID 10970735 DOI: 10.1006/Jmbi.2000.4014  0.345
2000 Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends in Biochemical Sciences. 25: 331-9. PMID 10871884 DOI: 10.1016/S0968-0004(00)01610-8  0.709
2000 Martí-Renom MA, Stote RH, Querol E, Aviles FX, Karplus M. Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints. Proteins. 40: 482-93. PMID 10861940 DOI: 10.1002/1097-0134(20000815)40:3<482::Aid-Prot150>3.0.Co;2-5  0.675
2000 Stultz CM, Karplus M. Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin. Proteins. 40: 258-89. PMID 10842341 DOI: 10.1002/(Sici)1097-0134(20000801)40:2<258::Aid-Prot80>3.0.Co;2-I  0.639
2000 Paci E, Karplus M. Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proceedings of the National Academy of Sciences of the United States of America. 97: 6521-6. PMID 10823892 DOI: 10.1073/Pnas.100124597  0.321
2000 Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Current Opinion in Structural Biology. 10: 139-45. PMID 10753811 DOI: 10.1016/S0959-440X(00)00063-4  0.64
2000 Caflisch A, Schramm HJ, Karplus M. Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach. Journal of Computer-Aided Molecular Design. 14: 161-79. PMID 10721504 DOI: 10.1023/A:1008146201260  0.488
2000 Vitkup D, Ringe D, Petsko GA, Karplus M. Solvent mobility and the protein 'glass' transition. Nature Structural Biology. 7: 34-8. PMID 10625424 DOI: 10.1038/71231  0.796
2000 Cui Q, Karplus M. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations The Journal of Chemical Physics. 112: 1133-1149. DOI: 10.1063/1.480658  0.607
2000 Karplus M. PROTEIN FOLDING: INSIGHTS FROM SIMULATIONS Biochemical Society Transactions. 28: A52-A52. DOI: 10.1042/Bst028A052A  0.343
2000 Cui Q, Karplus M. Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules The Journal of Physical Chemistry B. 104: 3721-3743. DOI: 10.1021/Jp994154G  0.591
2000 Karplus M. Aspects of Protein Reaction Dynamics:  Deviations from Simple Behavior The Journal of Physical Chemistry B. 104: 11-27. DOI: 10.1021/Jp993555T  0.348
2000 Reuter N, Dejaegere A, Maigret B, Karplus M. Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches The Journal of Physical Chemistry A. 104: 1720-1735. DOI: 10.1021/Jp9924124  0.756
2000 Stote RH, Dejaegere AP, Lefèvre J, Karplus M. Multiple Conformations of RGDW anddRGDW:  A Theoretical Study and Comparison with NMR Results The Journal of Physical Chemistry B. 104: 1624-1636. DOI: 10.1021/Jp992147M  0.667
2000 Petrella RJ, Karplus M. A Limiting-Case Study of Protein Structure Prediction:  Energy-Based Searches of Reduced Conformational Space The Journal of Physical Chemistry B. 104: 11370-11378. DOI: 10.1021/Jp001847K  0.324
2000 Mulholland AJ, Lyne PD, Karplus M. Ab Initio QM/MM Study of the Citrate Synthase Mechanism. A Low-Barrier Hydrogen Bond Is not Involved Journal of the American Chemical Society. 122: 534-535. DOI: 10.1021/Ja992874V  0.513
1999 Lazaridis T, Karplus M. Heat capacity and compactness of denatured proteins. Biophysical Chemistry. 78: 207-17. PMID 17030309 DOI: 10.1016/S0301-4622(99)00022-8  0.619
1999 Stultz CM, Karplus M. MCSS functionality maps for a flexible protein. Proteins. 37: 512-29. PMID 10651268 DOI: 10.1002/(Sici)1097-0134(19991201)37:4<512::Aid-Prot3>3.0.Co;2-O  0.66
1999 Dinner AR, Verosub E, Karplus M. Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly. Protein Engineering. 12: 909-17. PMID 10585496 DOI: 10.1093/Protein/12.11.909  0.597
1999 Zhou Y, Karplus M. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis. Journal of Molecular Biology. 293: 917-51. PMID 10543976 DOI: 10.1006/Jmbi.1999.2936  0.601
1999 Zhou Y, Karplus M. Interpreting the folding kinetics of helical proteins. Nature. 401: 400-3. PMID 10517642 DOI: 10.1038/43937  0.59
1999 Dinner AR, Karplus M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. Journal of Molecular Biology. 292: 403-19. PMID 10493884 DOI: 10.1006/Jmbi.1999.3051  0.617
1999 Blondel A, Renaud JP, Fischer S, Moras D, Karplus M. Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes. Journal of Molecular Biology. 291: 101-15. PMID 10438609 DOI: 10.1006/Jmbi.1999.2879  0.354
1999 Dinner AR, Lazaridis T, Karplus M. Understanding beta-hairpin formation. Proceedings of the National Academy of Sciences of the United States of America. 96: 9068-73. PMID 10430896 DOI: 10.1073/Pnas.96.16.9068  0.726
1999 Caflisch A, Karplus M. Structural details of urea binding to barnase: a molecular dynamics analysis. Structure (London, England : 1993). 7: 477-88. PMID 10378267 DOI: 10.1016/S0969-2126(99)80064-1  0.587
1999 Zhou Y, Hall CK, Karplus M. The calorimetric criterion for a two-state process revisited. Protein Science : a Publication of the Protein Society. 8: 1064-74. PMID 10338017 DOI: 10.1110/Ps.8.5.1064  0.534
1999 Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. Journal of Molecular Biology. 288: 477-87. PMID 10329155 DOI: 10.1006/Jmbi.1999.2685  0.664
1999 Paci E, Karplus M. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. Journal of Molecular Biology. 288: 441-59. PMID 10329153 DOI: 10.1006/Jmbi.1999.2670  0.386
1999 Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins. 35: 133-52. PMID 10223287 DOI: 10.1002/(Sici)1097-0134(19990501)35:2<133::Aid-Prot1>3.0.Co;2-N  0.686
1999 Dinner AR, Abkevich V, Shakhnovich E, Karplus M. Factors that affect the folding ability of proteins. Proteins. 35: 34-40. PMID 10090284 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<34::Aid-Prot4>3.0.Co;2-Q  0.693
1999 Dobson CM, Karplus M. The fundamentals of protein folding: bringing together theory and experiment. Current Opinion in Structural Biology. 9: 92-101. PMID 10047588 DOI: 10.1016/S0959-440X(99)80012-8  0.467
1999 Zhou Y, Vitkup D, Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology. 285: 1371-5. PMID 9917381 DOI: 10.1006/Jmbi.1998.2374  0.757
1999 Bartels C, Stote RH, Karplus M. Characterization of flexible molecules in solution: the RGDW peptide. Journal of Molecular Biology. 284: 1641-60. PMID 9878376 DOI: 10.1006/Jmbi.1998.2255  0.682
1999 Schaefer M, Bartels C, Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. Journal of Molecular Biology. 284: 835-48. PMID 9826519 DOI: 10.1006/Jmbi.1998.2172  0.399
1999 Martí-Renom MA, Stote RH, Querol E, Avilés FX, Karplus M. Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints. Journal of Molecular Biology. 284: 145-72. PMID 9811548 DOI: 10.1006/Jmbi.1998.2071  0.689
1999 Bartels C, Schaefer M, Karplus M. Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling The Journal of Chemical Physics. 111: 8048-8067. DOI: 10.1063/1.480139  0.35
1999 York DM, Karplus M. A Smooth Solvation Potential Based on the Conductor-Like Screening Model The Journal of Physical Chemistry A. 103: 11060-11079. DOI: 10.1021/Jp992097L  0.308
1999 Simonson T, Archontis G, Karplus M. A Poisson−Boltzmann Study of Charge Insertion in an Enzyme Active Site:  The Effect of Dielectric Relaxation The Journal of Physical Chemistry B. 103: 6142-6156. DOI: 10.1021/Jp991354J  0.709
1999 Dinner AR, Karplus M. The Thermodynamics and Kinetics of Protein Folding:  A Lattice Model Analysis of Multiple Pathways with Intermediates The Journal of Physical Chemistry B. 103: 7976-7994. DOI: 10.1021/Jp990851X  0.644
1999 van Vlijmen HWT, Karplus M. Analysis of Calculated Normal Modes of a Set of Native and Partially Unfolded Proteins The Journal of Physical Chemistry B. 103: 3009-3021. DOI: 10.1021/Jp983452V  0.354
1999 Lyne PD, Hodoscek M, Karplus M. A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region The Journal of Physical Chemistry A. 103: 3462-3471. DOI: 10.1021/Jp982115J  0.306
1999 Boresch S, Karplus M. The Role of Bonded Terms in Free Energy Simulations. 2. Calculation of Their Influence on Free Energy Differences of Solvation The Journal of Physical Chemistry A. 103: 119-136. DOI: 10.1021/Jp981629F  0.688
1999 Boresch S, Karplus M. The Role of Bonded Terms in Free Energy Simulations:  1. Theoretical Analysis The Journal of Physical Chemistry A. 103: 103-118. DOI: 10.1021/Jp981628N  0.674
1999 Buck M, Karplus M. Internal and Overall Peptide Group Motion in Proteins:  Molecular Dynamics Simulations for Lysozyme Compared with Results from X-ray and NMR Spectroscopy Journal of the American Chemical Society. 121: 9645-9658. DOI: 10.1021/Ja991309P  0.366
1999 Lopez X, Dejaegere A, Karplus M. Mechanism of Alkaline Hydrolysis of Cyclic and Acyclic Sulfates:  An ab Initio Study with Solvation Correction Journal of the American Chemical Society. 121: 5548-5558. DOI: 10.1021/Ja984193Q  0.66
1999 Schaefer M, Bartels C, Karplus M. Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 101: 194-204. DOI: 10.1007/S002140050429  0.38
1999 Bartels C, Schaefer M, Karplus M. Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 101: 62-66. DOI: 10.1007/S002140050407  0.376
1998 Dobson CM, Šali A, Karplus M. Protein Folding: A Perspective from Theory and Experiment. Angewandte Chemie (International Ed. in English). 37: 868-893. PMID 29711488 DOI: 10.1002/(Sici)1521-3773(19980420)37:7<868::Aid-Anie868>3.0.Co;2-H  0.575
1998 MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, ... ... Karplus M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B. 102: 3586-616. PMID 24889800 DOI: 10.1021/Jp973084F  0.8
1998 Ma J, Zheng X, Schnappauf G, Braus G, Karplus M, Lipscomb WN. Yeast chorismate mutase in the R state: simulations of the active site. Proceedings of the National Academy of Sciences of the United States of America. 95: 14640-5. PMID 9843942 DOI: 10.1073/Pnas.95.25.14640  0.509
1998 Petrella RJ, Lazaridis T, Karplus M. Protein sidechain conformer prediction: a test of the energy function. Folding & Design. 3: 353-77. PMID 9806937 DOI: 10.1016/S1359-0278(98)00050-9  0.632
1998 Dinner AR, So SS, Karplus M. Use of quantitative structure-property relationships to predict the folding ability of model proteins. Proteins. 33: 177-203. PMID 9779787 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<177::Aid-Prot4>3.0.Co;2-G  0.603
1998 van Vlijmen HW, Schaefer M, Karplus M. Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure. Proteins. 33: 145-58. PMID 9779784 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<145::Aid-Prot1>3.0.Co;2-I  0.7
1998 Ma J, Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proceedings of the National Academy of Sciences of the United States of America. 95: 8502-7. PMID 9671707 DOI: 10.1073/Pnas.95.15.8502  0.342
1998 Schaefer M, van Vlijmen HW, Karplus M. Electrostatic contributions to molecular free energies in solution. Advances in Protein Chemistry. 51: 1-57. PMID 9615168 DOI: 10.1016/S0065-3233(08)60650-6  0.656
1998 Caves LSD, Evanseck JD, Karplus M. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin Protein Science. 7: 649-666. PMID 9541397 DOI: 10.1002/Pro.5560070314  0.684
1998 Dinner AR, Karplus M. A metastable state in folding simulations of a protein model. Nature Structural Biology. 5: 236-41. PMID 9501918 DOI: 10.1038/Nsb0398-236  0.606
1998 Archontis G, Simonson T, Moras D, Karplus M. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. Journal of Molecular Biology. 275: 823-46. PMID 9480772 DOI: 10.1006/Jmbi.1997.1470  0.711
1998 van Vlijmen HW, Curry S, Schaefer M, Karplus M. Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH. Journal of Molecular Biology. 275: 295-308. PMID 9466910 DOI: 10.1006/Jmbi.1997.1418  0.647
1998 Lazaridis T, Lee I, Karplus M. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Science : a Publication of the Protein Society. 6: 2589-605. PMID 9416608 DOI: 10.1002/Pro.5560061211  0.641
1998 Zhou Y, Karplus M. Folding thermodynamics of a model three-helix-bundle protein. Proceedings of the National Academy of Sciences of the United States of America. 94: 14429-32. PMID 9405629 DOI: 10.1073/Pnas.94.26.14429  0.582
1998 Ma J, Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. Journal of Molecular Biology. 274: 114-31. PMID 9398520 DOI: 10.1006/Jmbi.1997.1313  0.344
1998 Stultz CM, Karplus M. On the potential surface of the locally enhanced sampling approximation Journal of Chemical Physics. 109: 8809-8815. DOI: 10.1063/1.477551  0.611
1998 Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition The Journal of Chemical Physics. 108: 6466-6483. DOI: 10.1063/1.476053  0.643
1998 Bartels C, Karplus M. Probability Distributions for Complex Systems:  Adaptive Umbrella Sampling of the Potential Energy The Journal of Physical Chemistry B. 102: 865-880. DOI: 10.1021/Jp972280J  0.383
1998 Dobson C, Šali A, Karplus M. Proteinfaltung aus theoretischer und experimenteller Sicht Angewandte Chemie. 110: 908-935. DOI: 10.1002/(Sici)1521-3757(19980403)110:7<908::Aid-Ange908>3.0.Co;2-0  0.508
1997 Lazaridis T, Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science (New York, N.Y.). 278: 1928-31. PMID 9395391 DOI: 10.1126/Science.278.5345.1928  0.66
1997 Ma J, Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proceedings of the National Academy of Sciences of the United States of America. 94: 11905-10. PMID 9342335 DOI: 10.1073/Pnas.94.22.11905  0.37
1997 Karplus M. The Levinthal paradox: yesterday and today. Folding & Design. 2: S69-75. PMID 9269572 DOI: 10.1016/S1359-0278(97)00067-9  0.37
1997 Vitkup D, Petsko GA, Karplus M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nature Structural Biology. 4: 202-8. PMID 9164461 DOI: 10.1038/Nsb0397-202  0.731
1997 van Vlijmen HW, Karplus M. PDB-based protein loop prediction: parameters for selection and methods for optimization. Journal of Molecular Biology. 267: 975-1001. PMID 9135125 DOI: 10.1006/Jmbi.1996.0857  0.658
1997 Watanabe M, Rosenbusch J, Schirmer T, Karplus M. Computer simulations of the OmpF porin from the outer membrane of Escherichia coli. Biophysical Journal. 72: 2094-102. PMID 9129811 DOI: 10.1016/S0006-3495(97)78852-0  0.359
1997 Zhou Y, Karplus M, Wichert JM, Hall CK. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions The Journal of Chemical Physics. 107: 10691-10708. DOI: 10.1063/1.474186  0.557
1997 Becker OM, Karplus M. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics The Journal of Chemical Physics. 106: 1495-1517. DOI: 10.1063/1.473299  0.335
1997 Simonson T, Archontis G, Karplus M. Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding. The Journal of Physical Chemistry B. 101: 8349-8362. DOI: 10.1021/Jp9711499  0.68
1997 Schaefer M, Sommer M, Karplus M. pH-Dependence of Protein Stability:  Absolute Electrostatic Free Energy Differences between Conformations† The Journal of Physical Chemistry B. 101: 1663-1683. DOI: 10.1021/Jp962972S  0.36
1997 Bartels C, Karplus M. Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations Journal of Computational Chemistry. 18: 1450-1462. DOI: 10.1002/(Sici)1096-987X(199709)18:12<1450::Aid-Jcc3>3.0.Co;2-I  0.342
1997 Caflisch A, Fischer S, Karplus M. Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex Journal of Computational Chemistry. 18: 723-743. DOI: 10.1002/(Sici)1096-987X(19970430)18:6<723::Aid-Jcc1>3.0.Co;2-U  0.594
1996 Zhou Y, Hall CK, Karplus M. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model. Physical Review Letters. 77: 2822-2825. PMID 10062054 DOI: 10.1103/Physrevlett.77.2822  0.531
1996 Karplus M, Ichiye T. Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations". Journal of Molecular Biology. 263: 120-2. PMID 8913294 DOI: 10.1006/Jmbi.1996.0562  0.353
1996 Miranker A, Karplus M. An automated method for dynamic ligand design. Proteins. 23: 472-90. PMID 8749844 DOI: 10.1002/Prot.340230403  0.325
1996 Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins: role of native structure. Proceedings of the National Academy of Sciences of the United States of America. 93: 8356-61. PMID 8710875 DOI: 10.1073/Pnas.93.16.8356  0.686
1996 Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 23: 318-26. PMID 8710825 DOI: 10.1002/Prot.340230306  0.716
1996 Mulholland AJ, Karplus M. Simulations of enzymic reactions. Biochemical Society Transactions. 24: 247-54. PMID 8674677 DOI: 10.1042/Bst0240247  0.517
1996 Lazaridis T, Archontis G, Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Advances in Protein Chemistry. 47: 231-306. PMID 8561050 DOI: 10.1016/S0065-3233(08)60547-1  0.792
1996 Stote RH, Karplus M. Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins. 23: 12-31. PMID 8539245 DOI: 10.1002/Prot.340230104  0.69
1996 ZHOU Y, KARPLUS M. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers Molecular Physics. 89: 1707-1717. DOI: 10.1080/00268979609482568  0.476
1996 Archontis G, Karplus M. Cumulant expansion of the free energy: Application to free energy derivatives and component analysis The Journal of Chemical Physics. 105: 11246-11260. DOI: 10.1063/1.472921  0.68
1996 Neria E, Karplus M. A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM) The Journal of Chemical Physics. 105: 10812-10818. DOI: 10.1063/1.472889  0.334
1996 Boresch S, Karplus M. The Jacobian factor in free energy simulations The Journal of Chemical Physics. 105: 5145-5154. DOI: 10.1063/1.472358  0.678
1996 Lazaridis T, Karplus M. Orientational correlations and entropy in liquid water The Journal of Chemical Physics. 105: 4294-4316. DOI: 10.1063/1.472247  0.608
1996 Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems The Journal of Chemical Physics. 105: 1902-1921. DOI: 10.1063/1.472061  0.357
1996 Schaefer M, Karplus M. A Comprehensive Analytical Treatment of Continuum Electrostatics The Journal of Physical Chemistry. 100: 1578-1599. DOI: 10.1021/Jp9521621  0.351
1996 Schmidt RK, Karplus M, Brady JW. The Anomeric Equilibrium ind-Xylose: Free Energy and the Role of Solvent Structuring Journal of the American Chemical Society. 118: 541-546. DOI: 10.1021/Ja951066A  0.373
1996 Blondel A, Karplus M. New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities Journal of Computational Chemistry. 17: 1132-1141. DOI: 10.1002/(Sici)1096-987X(19960715)17:9<1132::Aid-Jcc5>3.0.Co;2-T  0.306
1995 Joseph-McCarthy D, Petsko GA, Karplus M. Use of a minimum perturbation approach to predict TIM mutant structures. Protein Engineering. 8: 1103-15. PMID 8819976 DOI: 10.1093/Protein/8.11.1103  0.535
1995 Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Current Opinion in Structural Biology. 5: 58-73. PMID 7773748 DOI: 10.1016/0959-440X(95)80010-X  0.571
1995 MacKerell AD, Sommer MS, Karplus M. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis. Journal of Molecular Biology. 247: 774-807. PMID 7723031 DOI: 10.1016/S0022-2836(05)80155-X  0.595
1995 Matsumoto R, Sali A, Ghildyal N, Karplus M, Stevens RL. Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans. The Journal of Biological Chemistry. 270: 19524-31. PMID 7642636 DOI: 10.1074/Jbc.270.33.19524  0.494
1995 Caflisch A, Karplus M. Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. Journal of Molecular Biology. 252: 672-708. PMID 7563082 DOI: 10.1006/Jmbi.1995.0528  0.585
1995 Roux B, Prod'hom B, Karplus M. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophysical Journal. 68: 876-92. PMID 7538804 DOI: 10.1016/S0006-3495(95)80264-X  0.536
1995 Boresch S, Karplus M. The meaning of component analysis: decomposition of the free energy in terms of specific interactions. Journal of Molecular Biology. 254: 801-7. PMID 7500351 DOI: 10.1006/Jmbi.1995.0656  0.674
1995 Xu D, Schulten K, Becker OM, Karplus M. Temperature quench echoes in proteins The Journal of Chemical Physics. 103: 3112-3123. DOI: 10.1063/1.470270  0.615
1995 Karplus M, S˘ali A, Shakhnovich E. Kinetics of protein folding Nature. 373: 665-665. DOI: 10.1038/373665A0  0.518
1995 MacKerell AD, Wiorkiewicz-Kuczera J, Karplus M. An all-atom empirical energy function for the simulation of nucleic acids Journal of the American Chemical Society. 117: 11946-11975. DOI: 10.1021/Ja00153A017  0.317
1995 Caflisch A, Karplus M. Computational combinatorial chemistry for de novo ligand design: Review and assessment Perspectives in Drug Discovery and Design. 3: 51-84. DOI: 10.1007/Bf02174467  0.499
1995 Karplus M, Caflisch A, Săli A, Shakhnovich E. Protein dynamics: From the native to the unfolded state and back again Molecular Engineering. 5: 55-70. DOI: 10.1007/Bf00999578  0.7
1995 Brooks BR, Jane?i? D, Karplus M. Harmonic analysis of large systems. I. Methodology Journal of Computational Chemistry. 16: 1522-1542. DOI: 10.1002/Jcc.540161209  0.495
1995 Roux B, Karplus M. Potential energy function for cation-peptide interactions: Anab initio study Journal of Computational Chemistry. 16: 690-704. DOI: 10.1002/Jcc.540160605  0.612
1994 Mattos C, Petsko GA, Karplus M. Analysis of two-residue turns in proteins Journal of Molecular Biology. 238: 733-747. PMID 8182746 DOI: 10.1006/Jmbi.1994.1332  0.691
1994 Tidor B, Karplus M. The contribution of vibrational entropy to molecular association. The dimerization of insulin. Journal of Molecular Biology. 238: 405-14. PMID 8176732 DOI: 10.1006/Jmbi.1994.1300  0.589
1994 Caflisch A, Karplus M. Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proceedings of the National Academy of Sciences of the United States of America. 91: 1746-50. PMID 8127876 DOI: 10.1073/Pnas.91.5.1746  0.586
1994 Lau FT, Karplus M. Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant. Journal of Molecular Biology. 236: 1049-66. PMID 8120886 DOI: 10.1016/0022-2836(94)90011-6  0.398
1994 Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. Journal of Molecular Biology. 235: 1614-36. PMID 8107095 DOI: 10.1006/Jmbi.1994.1110  0.652
1994 Karplus M, Weaver DL. Protein folding dynamics: the diffusion-collision model and experimental data. Protein Science : a Publication of the Protein Society. 3: 650-68. PMID 8003983 DOI: 10.1002/Pro.5560030413  0.574
1994 Eisen MB, Wiley DC, Karplus M, Hubbard RE. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins. 19: 199-221. PMID 7937734 DOI: 10.1002/Prot.340190305  0.308
1994 Boresch S, Archontis G, Karplus M. Free energy simulations: the meaning of the individual contributions from a component analysis. Proteins. 20: 25-33. PMID 7824520 DOI: 10.1002/Prot.340200105  0.804
1994 Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 369: 248-51. PMID 7710478 DOI: 10.1038/369248A0  0.638
1994 Dunbrack RL, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature Structural Biology. 1: 334-40. PMID 7664040 DOI: 10.1038/Nsb0594-334  0.605
1994 Roux B, Karplus M. Molecular dynamics simulations of the gramicidin channel. Annual Review of Biophysics and Biomolecular Structure. 23: 731-61. PMID 7522667 DOI: 10.1146/Annurev.Bb.23.060194.003503  0.519
1994 Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations The Journal of Chemical Physics. 101: 1444-1451. DOI: 10.1063/1.467769  0.738
1994 Dejaegere A, Liang X, Karplus M. Phosphate ester hydrolysis: calculation of gas-phase reaction paths and solvation effects Journal of the Chemical Society, Faraday Transactions. 90: 1763. DOI: 10.1039/Ft9949001763  0.663
1994 Fischer S, Dunbrack RL, Karplus M. Cis-Trans Imide Isomerization of the Proline Dipeptide Journal of the American Chemical Society. 116: 11931-11937. DOI: 10.1021/Ja00105A036  0.509
1994 Straub JE, Lim C, Karplus M. Simulation Analysis of the Binding Interactions in the RNase A/3'-UMP Enzyme-Product Complex as a Function of pH Journal of the American Chemical Society. 116: 2591-2599. DOI: 10.1021/Ja00085A045  0.651
1994 Guo H, Karplus M. Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect The Journal of Physical Chemistry. 98: 7104-7105. DOI: 10.1021/J100080A002  0.408
1994 Nardi F, Doster W, Tidor B, Karplus M, Cusack S, Smith J. Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis Israel Journal of Chemistry. 34: 233-238. DOI: 10.1002/Ijch.199400026  0.744
1993 Becker OM, Karplus M. Temperature echoes in molecular dynamics simulations of proteins. Physical Review Letters. 70: 3514-3517. PMID 10053888 DOI: 10.1103/Physrevlett.70.3514  0.351
1993 Kuczera K, Lambry JC, Martin JL, Karplus M. Nonexponential relaxation after ligand dissociation from myoglobin: A molecular dynamics simulation Proceedings of the National Academy of Sciences of the United States of America. 90: 5805-5807. PMID 8516332 DOI: 10.1073/Pnas.90.12.5805  0.342
1993 Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. Journal of Molecular Biology. 230: 543-74. PMID 8464064 DOI: 10.1006/Jmbi.1993.1170  0.583
1993 Caflisch A, Miranker A, Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. Journal of Medicinal Chemistry. 36: 2142-67. PMID 8340918 DOI: 10.1021/Jm00067A013  0.539
1993 Nakagawa S, Yu HA, Karplus M, Umeyama H. Active site dynamics of acyl-chymotrypsin. Proteins. 16: 172-94. PMID 8332606 DOI: 10.1002/Prot.340160205  0.331
1993 Prod'hom B, Karplus M. The nature of the ion binding interactions in EF-hand peptide analogs: free energy simulation of Asp to Asn mutations. Protein Engineering. 6: 585-92. PMID 8234229 DOI: 10.1093/Protein/6.6.585  0.353
1993 Tidor B, Karplus M. The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state. Proteins. 15: 71-9. PMID 7680808 DOI: 10.1002/Prot.340150109  0.58
1993 Fischer S, Michnick S, Karplus M. A mechanism for rotamase catalysis by the FK506 binding protein (FKBP) Biochemistry. 32: 13830-13837. PMID 7505615 DOI: 10.1021/Bi00213A011  0.643
1993 Petsko G, Ringe D, Allen K, Lavie A, Gerhart-Mueller E, Clifton J, Hasson M, Fujita S, Sugio S, Xhang X, Davenport R, Lolis E, Neidhart D, Kenyon G, Gerlt J, ... ... Karplus M, et al. The structural enzymology of proton-transfer reactions Protein Engineering, Design and Selection. 6: 37. DOI: 10.1093/Protein/6.Supplement.37-A  0.631
1993 Watanabe M, Karplus M. Dynamics of molecules with internal degrees of freedom by multiple time‐step methods The Journal of Chemical Physics. 99: 8063-8074. DOI: 10.1063/1.465633  0.356
1993 Ferentz AE, Wiorkiewicz-Kuczera J, Karplus M, Verdine GL. Molecular dynamics simulations of disulfide cross-linked DNA decamers Journal of the American Chemical Society. 115: 7569-7583. DOI: 10.1021/Ja00070A002  0.338
1993 Dejaegere A, Karplus M. Hydrolysis rate difference between cyclic and acyclic phosphate esters: solvation versus strain Journal of the American Chemical Society. 115: 5316-5317. DOI: 10.1021/Ja00065A062  0.606
1993 Roux B, Karplus M. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane Journal of the American Chemical Society. 115: 3250-3262. DOI: 10.1021/Ja00061A025  0.581
1993 Smith PE, Pettitt BM, Karplus M. Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface The Journal of Physical Chemistry. 97: 6907-6913. DOI: 10.1021/J100128A027  0.727
1992 Miranker A, Karplus M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins. 11: 29-34. PMID 1961699 DOI: 10.1002/Prot.340110104  0.333
1992 Summers NL, Karplus M. Modeling of side chains, loops, and insertions in proteins. Methods in Enzymology. 202: 156-204. PMID 1784173 DOI: 10.1016/0076-6879(91)02011-W  0.348
1992 Ichiye T, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 11: 205-17. PMID 1749773 DOI: 10.1002/Prot.340110305  0.379
1992 Treutlein H, Schulten K, Brünger AT, Karplus M, Deisenhofer J, Michel H. Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study. Proceedings of the National Academy of Sciences of the United States of America. 89: 75-9. PMID 1729721 DOI: 10.1073/Pnas.89.1.75  0.618
1992 Yapa K, Weaver DL, Karplus M. Beta-sheet coil transitions in a simple polypeptide model. Proteins. 12: 237-65. PMID 1557351 DOI: 10.1002/Prot.340120304  0.618
1992 Karplus M, Evanseck JD, Joseph D, Bash PA, Field MJ. Simulation analysis of triose phosphate isomerase: Conformational transition and catalysis Faraday Discussions. 93: 239-248. PMID 1290934 DOI: 10.1039/Fd9929300239  0.754
1992 Lee S, Karplus M. Erratum: Kinetics of diffusion‐influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions [J. Chem. Phys. 86, 1883 (1987)] The Journal of Chemical Physics. 96: 1663-1663. DOI: 10.1063/1.462914  0.559
1992 Brueschweiler R, Roux B, Blackledge M, Griesinger C, Karplus M, Ernst RR. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution Journal of the American Chemical Society. 114: 2289-2302. DOI: 10.1021/Ja00033A002  0.605
1992 Smith JC, Karplus M. Empirical force field study of geometries and conformational transitions of some organic molecules Journal of the American Chemical Society. 114: 801-812. DOI: 10.1021/Ja00029A001  0.557
1992 Guo H, Karplus M. Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers The Journal of Physical Chemistry. 96: 7273-7287. DOI: 10.1021/J100197A027  0.438
1992 Guo H, Karplus M. Ab initio studies of methylated 1,3-butadienes Journal of Molecular Structure: Theochem. 260: 347-393. DOI: 10.1016/0166-1280(92)87055-5  0.429
1992 Fischer S, Karplus M. Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom Chemical Physics Letters. 194: 252-261. DOI: 10.1016/0009-2614(92)85543-J  0.35
1991 Shakhnovich E, Farztdinov G, Gutin A, Karplus M. Protein folding bottlenecks: A lattice Monte Carlo simulation. Physical Review Letters. 67: 1665-1668. PMID 10044213 DOI: 10.1103/Physrevlett.67.1665  0.57
1991 Bashford D, Karplus M. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 29: 10219-25. PMID 2271649 DOI: 10.1021/Bi00496A010  0.363
1991 Summers NL, Karplus M. Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations. Journal of Molecular Biology. 216: 991-1016. PMID 2266566 DOI: 10.1016/S0022-2836(99)80016-3  0.327
1991 Bash PA, Field MJ, Davenport RC, Petsko GA, Ringe D, Karplus M. Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry. 30: 5826-32. PMID 2043624 DOI: 10.1021/Bi00238A003  0.727
1991 Davenport RC, Bash PA, Seaton BA, Karplus M, Petsko GA, Ringe D. Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway. Biochemistry. 30: 5821-6. PMID 2043623 DOI: 10.1021/Bi00238A002  0.64
1991 Petrich JW, Lambry JC, Kuczera K, Karplus M, Poyart C, Martin JL. Ligand binding and protein relaxation in heme proteins: a room temperature analysis of NO geminate recombination. Biochemistry. 30: 3975-87. PMID 2018766 DOI: 10.1021/Bi00230A025  0.351
1991 Tidor B, Karplus M. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry. 30: 3217-28. PMID 2009262 DOI: 10.1021/Bi00227A009  0.598
1991 Miranker A, Radford SE, Karplus M, Dobson CM. Demonstration by NMR of folding domains in lysozyme. Nature. 349: 633-6. PMID 2000138 DOI: 10.1038/349633A0  0.488
1991 Pastor RW, Venable RM, Karplus M. Model for the structure of the lipid bilayer. Proceedings of the National Academy of Sciences of the United States of America. 88: 892-6. PMID 1992480 DOI: 10.1073/Pnas.88.3.892  0.328
1991 Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. Proceedings of the National Academy of Sciences of the United States of America. 88: 10880-4. PMID 1961758 DOI: 10.1073/Pnas.88.23.10880  0.713
1991 Kuriyan J, Osapay K, Burley SK, Brünger AT, Hendrickson WA, Karplus M. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins. 10: 340-58. PMID 1946343 DOI: 10.1002/Prot.340100407  0.556
1991 Karplus M, Prévost M, Tidor B, Wodak S. Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase. Ciba Foundation Symposium. 161: 63-74. PMID 1814697 DOI: 10.1002/9780470514146.ch5  0.664
1991 Pettitt BM, Matsunaga T, al-Obeidi F, Gehrig C, Hruby VJ, Karplus M. Dynamical search for bis-penicillamine enkephalin conformations. Biophysical Journal. 60: 1540-4. PMID 1777571 DOI: 10.1016/S0006-3495(91)82188-9  0.672
1991 Roux B, Karplus M. Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophysical Journal. 59: 961-81. PMID 1714305 DOI: 10.1016/S0006-3495(91)82311-6  0.605
1991 Rosen MK, Michnick SW, Karplus M, Schreiber SL. Proton and nitrogen sequential assignments and secondary structure determination of the human FK506 and rapamycin binding protein. Biochemistry. 30: 4774-89. PMID 1709363 DOI: 10.1021/Bi00233A020  0.597
1991 Michnick SW, Rosen MK, Wandless TJ, Karplus M, Schreiber SL. Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science (New York, N.Y.). 252: 836-9. PMID 1709301 DOI: 10.1126/Science.1709301  0.592
1991 Straub JE, Karplus M. Energy equipartitioning in the classical time‐dependent Hartree approximation The Journal of Chemical Physics. 94: 6737-6739. DOI: 10.1063/1.460250  0.679
1991 Guo H, Karplus M. Ab initio studies of polyenes. I. 1,3‐butadiene The Journal of Chemical Physics. 94: 3679-3699. DOI: 10.1063/1.459739  0.486
1991 Stote R, States D, Karplus M. On the treatment of electrostatic interactions in biomolecular simulation Journal De Chimie Physique. 88: 2419-2433. DOI: 10.1063/1.41345  0.773
1991 Prévost M, Wodak S, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability : molecular dynamics simulations of the lie → Ala mutation in Barnase Journal De Chimie Physique. 88: 2727-2728. DOI: 10.1051/Jcp/1991882727  0.718
1991 Garen J, Field M, Kneller G, Karplus M, Smith J. Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations Journal De Chimie Physique. 88: 2587-2596. DOI: 10.1051/Jcp/1991882587  0.709
1991 Yu HA, Karplus M, Pettitt BM. Aqueous solvation of N-methylacetamide conformers: comparison of simulations and integral equation theories Journal of the American Chemical Society. 113: 2425-2434. DOI: 10.1021/Ja00007A012  0.623
1991 Wandless TJ, Michnick SW, Rosen MK, Karplus M, Schreiber SL. FK506 and rapamycin binding to FKBP: common elements in immunophilin-ligand complexation Journal of the American Chemical Society. 113: 2339-2341. DOI: 10.1021/Ja00006A083  0.538
1991 Ha S, Gao J, Tidor B, Brady JW, Karplus M. Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis Journal of the American Chemical Society. 113: 1553-1557. DOI: 10.1021/Ja00005A015  0.739
1991 Bashford D, Karplus M. Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation The Journal of Physical Chemistry. 95: 9556-9561. DOI: 10.1021/J100176A093  0.31
1991 Lim C, Bashford D, Karplus M. Absolute pKa calculations with continuum dielectric methods The Journal of Physical Chemistry. 95: 5610-5620. DOI: 10.1021/J100167A045  0.352
1991 Roux B, Karplus M. Ion transport in a gramicidin-like channel: dynamics and mobility The Journal of Physical Chemistry. 95: 4856-4868. DOI: 10.1021/J100165A049  0.561
1991 Bruenger AT, Karplus M. Molecular dynamics simulations with experimental restraints Accounts of Chemical Research. 24: 54-61. DOI: 10.1021/Ar00002A005  0.354
1991 Straub JE, Karplus M. Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10 ps Chemical Physics. 158: 221-248. DOI: 10.1016/0301-0104(91)87068-7  0.689
1990 Summers NL, Karplus M. Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin. Journal of Molecular Biology. 210: 785-811. PMID 2693742 DOI: 10.1016/0022-2836(89)90109-5  0.357
1990 Joseph D, Petsko GA, Karplus M. Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science (New York, N.Y.). 249: 1425-8. PMID 2402636 DOI: 10.1126/Science.2402636  0.537
1990 Kuczera K, Kuriyan J, Karplus M. Temperature dependence of the structure and dynamics of myoglobin. A simulation approach. Journal of Molecular Biology. 213: 351-73. PMID 2342112 DOI: 10.1016/S0022-2836(05)80196-2  0.549
1990 Smith J, Kuczera K, Karplus M. Dynamics of myoglobin: Comparison of simulation results with neutron scattering spectra Proceedings of the National Academy of Sciences of the United States of America. 87: 1601-1605. PMID 2304919 DOI: 10.1073/Pnas.87.4.1601  0.588
1990 Kuczera K, Gao J, Tidor B, Karplus M. Free energy of sickling: A simulation analysis. Proceedings of the National Academy of Sciences of the United States of America. 87: 8481-5. PMID 2236057 DOI: 10.1073/Pnas.87.21.8481  0.759
1990 Straub JE, Karplus M. The interpretation of site-directed mutagenesis experiments by linear free energy relations. Protein Engineering. 3: 673-5. PMID 2217141 DOI: 10.1093/Protein/3.8.673  0.676
1990 Karplus M, Petsko GA. Molecular dynamics simulations in biology. Nature. 347: 631-9. PMID 2215695 DOI: 10.1038/347631A0  0.579
1990 Bruccoleri RE, Karplus M. Conformational sampling using high-temperature molecular dynamics. Biopolymers. 29: 1847-62. PMID 2207289 DOI: 10.1002/Bip.360291415  0.369
1990 Smith J, Cusack S, Tidor B, Karplus M. Inelastic neutron scattering analysis of low‐frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor The Journal of Chemical Physics. 93: 2974-2991. DOI: 10.1063/1.458885  0.729
1990 Coalson RD, Karplus M. Multidimensional variational Gaussian wave packet dynamics with application to photodissociation spectroscopy The Journal of Chemical Physics. 93: 3919-3930. DOI: 10.1063/1.458778  0.544
1990 Yu H, Roux B, Karplus M. Solvation thermodynamics: An approach from analytic temperature derivatives The Journal of Chemical Physics. 92: 5020-5033. DOI: 10.1063/1.458538  0.585
1990 Elber R, Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin Journal of the American Chemical Society. 112: 9161-9175. DOI: 10.1021/Ja00181A020  0.67
1990 Haydock K, Lim C, Brunger AT, Karplus M. Simulation analysis of structures on the reaction pathway of RNAse A Journal of the American Chemical Society. 112: 3826-3831. DOI: 10.1021/Ja00166A016  0.654
1990 Roux B, Yu HA, Karplus M. Molecular basis for the Born model of ion solvation The Journal of Physical Chemistry. 94: 4683-4688. DOI: 10.1021/J100374A057  0.591
1990 Gao J, Karplus M. A theoretical investigation of the AlC2H4 complex Chemical Physics Letters. 169: 410-415. DOI: 10.1016/0009-2614(90)87068-3  0.629
1990 Field MJ, Bash PA, Karplus M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations Journal of Computational Chemistry. 11: 700-733. DOI: 10.1002/Jcc.540110605  0.603
1990 Perahia D, Levy RM, Karplus M. Motions of an ?-helical polypeptide: Comparison of molecular and harmonic dynamics Biopolymers. 29: 645-677. DOI: 10.1002/Bip.360290402  0.643
1989 Bashford D, Karplus M, Canters GW. Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis. Journal of Molecular Biology. 203: 507-10. PMID 3199443 DOI: 10.1016/0022-2836(88)90016-2  0.316
1989 Post CB, Dobson CM, Karplus M. A molecular dynamics analysis of protein structural elements. Proteins. 5: 337-54. PMID 2798410 DOI: 10.1002/Prot.340050409  0.53
1989 Brooks CL, Karplus M. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. Journal of Molecular Biology. 208: 159-81. PMID 2769750 DOI: 10.1016/0022-2836(89)90093-4  0.556
1989 Gao J, Kuczera K, Tidor B, Karplus M. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science (New York, N.Y.). 244: 1069-72. PMID 2727695 DOI: 10.1126/Science.2727695  0.764
1989 Weiss MA, Nguyen DT, Khait I, Inouye K, Frank BH, Beckage M, O'Shea E, Shoelson SE, Karplus M, Neuringer LJ. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics. Biochemistry. 28: 9855-73. PMID 2692717 DOI: 10.1021/Bi00451A046  0.343
1989 Kuriyan J, Brünger AT, Karplus M, Hendrickson WA. X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin. Acta Crystallographica. Section a, Foundations of Crystallography. 45: 396-409. PMID 2619971 DOI: 10.1107/S0108767389000437  0.511
1989 Brünger AT, Karplus M, Petsko GA. Crystallographic refinement by simulated annealing: application to crambin Acta Crystallographica Section a Foundations of Crystallography. 45: 50-61. DOI: 10.1107/S0108767388009195  0.513
1989 Pastor RW, Karplus M. Inertial effects in butane stochastic dynamics The Journal of Chemical Physics. 91: 211-218. DOI: 10.1063/1.457508  0.308
1989 Guo H, Karplus M. Basis set and polarization function effects on optimized geometries and harmonic frequencies at the second‐order Mo/ller–Plesset perturbation level The Journal of Chemical Physics. 91: 1719-1733. DOI: 10.1063/1.457079  0.437
1989 Smith J, Kuczera K, Tidor B, Doster W, Cusack S, Karplus M. Internal dynamics of globular proteins: Comparison of neutron scattering measurements and theoretical models Physica B: Physics of Condensed Matter. 156: 437-443. DOI: 10.1016/0921-4526(89)90699-6  0.757
1988 Ichiye T, Karplus M. Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation. Proteins. 2: 236-59. PMID 3447180 DOI: 10.1002/Prot.340020308  0.355
1988 Ichiye T, Karplus M. Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis. Biochemistry. 27: 3487-97. PMID 3390447 DOI: 10.1021/Bi00409A054  0.347
1988 Bashford D, Cohen FE, Karplus M, Kuntz ID, Weaver DL. Diffusion-collision model for the folding kinetics of myoglobin. Proteins. 4: 211-27. PMID 3237719 DOI: 10.1002/Prot.340040308  0.678
1988 Brünger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins. 4: 148-56. PMID 3227015 DOI: 10.1002/Prot.340040208  0.371
1988 Cusack S, Smith J, Finney J, Tidor B, Karplus M. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. Journal of Molecular Biology. 202: 903-8. PMID 2459399 DOI: 10.1016/0022-2836(88)90566-9  0.754
1988 Roux B, Karplus M. The normal modes of the gramicidin-A dimer channel. Biophysical Journal. 53: 297-309. PMID 2450595 DOI: 10.1016/S0006-3495(88)83107-2  0.591
1988 Pastor RW, Venable RM, Karplus M, Szabo A. A simulation based model of NMRT1relaxation in lipid bilayer vesicles The Journal of Chemical Physics. 89: 1128-1140. DOI: 10.1063/1.455219  0.304
1988 Pastor RW, Venable RM, Karplus M. Brownian dynamics simulation of a lipid chain in a membrane bilayer The Journal of Chemical Physics. 89: 1112-1127. DOI: 10.1063/1.455218  0.333
1988 Yu H, Karplus M. A thermodynamic analysis of solvation The Journal of Chemical Physics. 89: 2366-2379. DOI: 10.1063/1.455080  0.338
1988 Guo H, Karplus M. Ab initio force field for the planar vibrations of benzene The Journal of Chemical Physics. 89: 4235-4245. DOI: 10.1063/1.454808  0.43
1988 Hruby VJ, Kao LF, Pettitt BM, Karplus M. The conformational properties of the delta opioid peptide [cyclic] [D-pen2,D-pen5]enkephalin in aqueous solution determined by NMR and energy minimization calculations Journal of the American Chemical Society. 110: 3351-3359. DOI: 10.1021/Ja00219A002  0.623
1988 Pettitt BM, Karplus M. Conformational free energy of hydration for the alanine dipeptide: thermodynamic analysis The Journal of Physical Chemistry. 92: 3994-3997. DOI: 10.1021/J100324A061  0.658
1988 Lee S, Karplus M. Dynamics of reactions involving diffusive multidimensional barrier crossing The Journal of Physical Chemistry. 92: 1075-1086. DOI: 10.1021/J100316A018  0.565
1988 Hemley RJ, Lasaga AC, Vaida V, Karplus M. Theoretical analysis of the 11Bu+ (1B1+) .rarw. 11Ag- (1A1-) transition of trans- and cis-1,3,5-hexatriene The Journal of Physical Chemistry. 92: 945-954. DOI: 10.1021/J100315A018  0.643
1988 Chen LXQ, Engh RA, Bruenger AT, Nguyen DT, Karplus M, Fleming GR. Dynamics simulation studies of apoazurin of Alcaligenes denitrificans Biochemistry. 27: 6908-6921. DOI: 10.1021/Bi00418A037  0.329
1988 Bash P, Field M, Karplus M. A quantum molecular dynamic free energy perturbation method applied to chemical reactions in the condensed phase Journal of Molecular Graphics. 6: 219. DOI: 10.1016/S0263-7855(98)80029-5  0.332
1988 HRUBY VJ, KAO L, PETTITT BM, KARPLUS M. ChemInform Abstract: Conformational Properties of the Delta Opioid Peptide Cyclic(D-Pen2,D-Pen5)enkephalin in Aqueous Solution Determined by NMR and Energy Minimization Calculations. Cheminform. 19. DOI: 10.1002/chin.198838055  0.589
1988 HEMLEY RJ, LASAGA AC, VAIDA V, KARPLUS M. ChemInform Abstract: Theoretical Analysis of the 11B+ u (1B+ 1) ← 11A- g (1A- 1) Transition of trans- and cis-1,3,5-Hexatriene Cheminform. 19. DOI: 10.1002/chin.198824042  0.407
1987 Brünger AT, Kuriyan J, Karplus M. Crystallographic R factor refinement by molecular dynamics. Science (New York, N.Y.). 235: 458-60. PMID 17810339 DOI: 10.1126/Science.235.4787.458  0.751
1987 Brünger AT, Campbell RL, Clore GM, Gronenborn AM, Karplus M, Petsko GA, Teeter MM. Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints. Science (New York, N.Y.). 235: 1049-53. PMID 17782253 DOI: 10.1126/Science.235.4792.1049  0.72
1987 Frauenfelder H, Hartmann H, Karplus M, Kuntz ID, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RF, Connolly ML. Thermal expansion of a protein. Biochemistry. 26: 254-61. PMID 3828301 DOI: 10.1021/Bi00375A035  0.701
1987 Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers. 26: 137-68. PMID 3801593 DOI: 10.1002/Bip.360260114  0.352
1987 Elber R, Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science (New York, N.Y.). 235: 318-21. PMID 3798113 DOI: 10.1126/Science.3798113  0.727
1987 Brünger AT, Huber R, Karplus M. Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain. Biochemistry. 26: 5153-62. PMID 3663651 DOI: 10.1021/Bi00390A039  0.345
1987 Nilges M, Clore GM, Gronenborn AM, Brunger AT, Karplus M, Nilsson L. Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 26: 3718-33. PMID 3651407 DOI: 10.1021/bi00386a068  0.664
1987 Lee SY, Karplus M, Bashford D, Weaver D. Brownian dynamics simulation of protein folding: a study of the diffusion-collision model. Biopolymers. 26: 481-506. PMID 3567323 DOI: 10.1002/Bip.360260404  0.733
1987 Nadler W, Brünger AT, Schulten K, Karplus M. Molecular and stochastic dynamics of proteins. Proceedings of the National Academy of Sciences of the United States of America. 84: 7933-7. PMID 3479772 DOI: 10.1073/Pnas.84.22.7933  0.609
1987 Karplus M. Molecular dynamics: applications to proteins. Annals of the New York Academy of Sciences. 482: 255-66. PMID 3471110 DOI: 10.1111/J.1749-6632.1986.Tb20959.X  0.344
1987 Karplus M, Brünger AT, Elber R, Kuriyan J. Molecular dynamics: applications to proteins. Cold Spring Harbor Symposia On Quantitative Biology. 52: 381-90. PMID 3454267 DOI: 10.1101/Sqb.1987.052.01.044  0.755
1987 Kuriyan J, Karplus M, Petsko GA. Estimation of uncertainties in X-ray refinement results by use of perturbed structures. Proteins. 2: 1-12. PMID 3447165 DOI: 10.1002/Prot.340020102  0.613
1987 Karplus M, Ichiye T, Pettitt BM. Configurational entropy of native proteins. Biophysical Journal. 52: 1083-5. PMID 3427197 DOI: 10.1016/S0006-3495(87)83303-9  0.666
1987 Summers NL, Carlson WD, Karplus M. Analysis of side-chain orientations in homologous proteins. Journal of Molecular Biology. 196: 175-98. PMID 3309349 DOI: 10.1016/0022-2836(87)90520-1  0.329
1987 Clore GM, Nilges M, Brünger AT, Karplus M, Gronenborn AM. A comparison of the restrained molecular dynamics and distance geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances. Febs Letters. 213: 269-77. PMID 3030815 DOI: 10.1016/0014-5793(87)81504-1  0.384
1987 Weiss MA, Pabo CO, Karplus M, Sauer RT. Dimerization of the operator binding domain of phage lambda repressor. Biochemistry. 26: 897-904. PMID 2952164 DOI: 10.1021/Bi00377A034  0.316
1987 Brünger AT, Clore GM, Gronenborn AM, Karplus M. Solution conformations of human growth hormone releasing factor: comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance data. Protein Engineering. 1: 399-406. PMID 2854259 DOI: 10.1093/Protein/1.5.399  0.362
1987 Delepierre M, Dobson CM, Karplus M, Poulsen FM, States DJ, Wedin RE. Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme. Journal of Molecular Biology. 197: 111-30. PMID 2824793 DOI: 10.1016/0022-2836(87)90613-9  0.666
1987 Carlson WD, Handschumacher M, Summers N, Karplus M, Haber E. Models for the three-dimensional structure of renin inhibitors bound in the active site of human renin: an analysis of the properties that produce tight binding. Journal of Cardiovascular Pharmacology. 10: S91-3. PMID 2485071 DOI: 10.1097/00005344-198706107-00015  0.323
1987 States DJ, Creighton TE, Dobson CM, Karplus M. Conformations of intermediates in the folding of the pancreatic trypsin inhibitor. Journal of Molecular Biology. 195: 731-9. PMID 2443711 DOI: 10.1016/0022-2836(87)90192-6  0.678
1987 Karplus M. Molecular Dynamics Simulations of Proteins Physics Today. 40: 68-72. DOI: 10.1063/1.881116  0.388
1987 Lee S, Karplus M. Kinetics of diffusion‐influenced bimolecular reactions in solution. II. Effects of the gating mode and orientation‐dependent reactivity The Journal of Chemical Physics. 86: 1904-1921. DOI: 10.1063/1.452757  0.587
1987 Lee S, Karplus M. Kinetics of diffusion‐influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions The Journal of Chemical Physics. 86: 1883-1903. DOI: 10.1063/1.452140  0.571
1987 Bash PA, Field MJ, Karplus M. Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential Journal of the American Chemical Society. 109: 8092-8094. DOI: 10.1021/Ja00260A028  0.584
1987 States DJ, Karplus M. A model for electrostatic effects in proteins Journal of Molecular Biology. 197: 122-130. DOI: 10.1016/0022-2836(87)90614-0  0.604
1987 Elber R, Karplus M. A method for determining reaction paths in large molecules: Application to myoglobin Chemical Physics Letters. 139: 375-380. DOI: 10.1016/0009-2614(87)80576-6  0.684
1987 Montgomery Pettitt B, Karplus M. The structure of water surrounding a peptide: a theoretical approach Chemical Physics Letters. 136: 383-386. DOI: 10.1016/0009-2614(87)80271-3  0.337
1986 Clore GM, Nilges M, Sukumaran DK, Brünger AT, Karplus M, Gronenborn AM. The three-dimensional structure of alpha1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. The Embo Journal. 5: 2729-35. PMID 16453716 DOI: 10.1002/J.1460-2075.1986.Tb04557.X  0.668
1986 Kuriyan J, Wilz S, Karplus M, Petsko GA. X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. Journal of Molecular Biology. 192: 133-54. PMID 3820301 DOI: 10.1016/0022-2836(86)90470-5  0.619
1986 Kuriyan J, Petsko GA, Levy RM, Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. Journal of Molecular Biology. 190: 227-54. PMID 3795269 DOI: 10.1016/0022-2836(86)90295-0  0.716
1986 Post CB, Brooks BR, Karplus M, Dobson CM, Artymiuk PJ, Cheetham JC, Phillips DC. Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations. Journal of Molecular Biology. 190: 455-79. PMID 3783708 DOI: 10.1016/0022-2836(86)90015-X  0.643
1986 Ichiye T, Olafson BD, Swaminathan S, Karplus M. Structure and internal mobility of proteins: a molecular dynamics study of hen egg white lysozyme. Biopolymers. 25: 1909-37. PMID 3779015 DOI: 10.1002/Bip.360251008  0.392
1986 Dobson CM, Karplus M. Internal motion of proteins: nuclear magnetic resonance measurements and dynamic simulations. Methods in Enzymology. 131: 362-89. PMID 3773766 DOI: 10.1016/0076-6879(86)31049-8  0.365
1986 Karplus M. Internal dynamics of proteins. Methods in Enzymology. 131: 283-307. PMID 3773762 DOI: 10.1016/0076-6879(86)31046-2  0.327
1986 Brooks CL, Karplus M. Theoretical approaches to solvation of biopolymers. Methods in Enzymology. 127: 369-400. PMID 3736426 DOI: 10.1016/0076-6879(86)27031-7  0.545
1986 Brünger AT, Clore GM, Gronenborn AM, Karplus M. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proceedings of the National Academy of Sciences of the United States of America. 83: 3801-5. PMID 3459158 DOI: 10.1073/Pnas.83.11.3801  0.364
1986 Clore GM, Brünger AT, Karplus M, Gronenborn AM. Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin. Journal of Molecular Biology. 191: 523-51. PMID 3029386 DOI: 10.1016/0022-2836(86)90146-4  0.369
1986 Nilsson L, Clore GM, Gronenborn AM, Brünger AT, Karplus M. Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2. Journal of Molecular Biology. 188: 455-75. PMID 3016285 DOI: 10.1016/0022-2836(86)90168-3  0.32
1986 Karplus M, McCammon JA. The dynamics of proteins. Scientific American. 254: 42-51. PMID 2938253 DOI: 10.1038/Scientificamerican0486-42  0.474
1986 POST CB, KARPLUS M, DOBSON C. A Lysozyme Molecular Dynamics Simulation Annals of the New York Academy of Sciences. 482: 267-268. DOI: 10.1111/J.1749-6632.1986.Tb20960.X  0.484
1986 Hemley RJ, Brooks BR, Karplus M. Theoretical study of the ground‐state vibrations of the linear polyenes The Journal of Chemical Physics. 85: 6550-6564. DOI: 10.1063/1.451437  0.665
1986 Smith J, Cusack S, Pezzeca U, Brooks B, Karplus M. Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor The Journal of Chemical Physics. 85: 3636-3654. DOI: 10.1063/1.450935  0.73
1986 Post CB, Karplus M. Does lysozyme follow the lysozyme pathway? An alternative based on dynamic, structural, and stereoelectronic considerations Journal of the American Chemical Society. 108: 1317-1319. DOI: 10.1021/Ja00266A044  0.323
1986 Pettitt BM, Karplus M, Rossky PJ. Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules The Journal of Physical Chemistry. 90: 6335-6345. DOI: 10.1021/J100281A055  0.749
1986 Cusack S, Smith J, Finney J, Karplus M, Trewhella J. Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy Physica B+C. 136: 256-259. DOI: 10.1016/S0378-4363(86)80069-9  0.688
1986 Cusack S, Smith J, Finney J, Karplus M, Trewhella J. Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy Physica B+C. 136: 256-259. DOI: 10.1016/S0378-4363(86)80069-9  0.642
1986 Nilsson L, Karplus M, Brünger A, Clore M, Gronenbornt A. Determination of 3D molecular structures from NMR/NOE distance data: application to nucleic acids Journal of Molecular Graphics. 4: 182. DOI: 10.1016/0263-7855(86)80031-5  0.642
1986 Nilsson L, Karplus M. Empirical energy functions for energy minimization and dynamics of nucleic acids Journal of Computational Chemistry. 7: 591-616. DOI: 10.1002/Jcc.540070502  0.378
1986 Karplus M. Molecular Dynamics of Biomolecules: Overview and Applications Israel Journal of Chemistry. 27: 121-126. DOI: 10.1002/Ijch.198600021  0.309
1985 Hoch JC, Dobson CM, Karplus M. Vicinal coupling constants and protein dynamics Biochemistry. 24: 3831-3841. PMID 4052369 DOI: 10.1021/Bi00336A003  0.676
1985 Brünger AT, Brooks CL, Karplus M. Active site dynamics of ribonuclease. Proceedings of the National Academy of Sciences of the United States of America. 82: 8458-62. PMID 3866234 DOI: 10.1073/Pnas.82.24.8458  0.536
1985 Brooks B, Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proceedings of the National Academy of Sciences of the United States of America. 82: 4995-9. PMID 3860838 DOI: 10.1073/Pnas.82.15.4995  0.517
1985 Shih HH, Brady J, Karplus M. Structure of proteins with single-site mutations: a minimum perturbation approach. Proceedings of the National Academy of Sciences of the United States of America. 82: 1697-700. PMID 3856851 DOI: 10.1073/Pnas.82.6.1697  0.311
1985 Levy RM, Sheridan RP, Keepers JW, Dubey GS, Swaminathan S, Karplus M. Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. Biophysical Journal. 48: 509-18. PMID 3840041 DOI: 10.1016/S0006-3495(85)83806-6  0.572
1985 Irikura KK, Tidor B, Brooks BR, Karplus M. Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. Science (New York, N.Y.). 229: 571-2. PMID 3839596 DOI: 10.1126/Science.3839596  0.632
1985 Brooks CL, Brünger A, Karplus M. Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers. 24: 843-65. PMID 2410050 DOI: 10.1002/Bip.360240509  0.545
1985 KARPLUS M. Dynamic Aspects of Protein Structure Annals of the New York Academy of Sciences. 439: 107-123. DOI: 10.1111/J.1749-6632.1985.Tb25792.X  0.346
1985 Brooks CL, Pettitt BM, Karplus M. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids The Journal of Chemical Physics. 83: 5897-5908. DOI: 10.1063/1.449621  0.699
1985 Pettitt BM, Karplus M. The potential of mean force between polyatomic molecules in polar molecular solvents The Journal of Chemical Physics. 83: 781-789. DOI: 10.1063/1.449493  0.637
1985 Hemley RJ, Leopold DG, Vaida V, Karplus M. The singlet states of styrene. Theoretical vibrational analysis of the ultraviolet spectrum The Journal of Chemical Physics. 82: 5379-5397. DOI: 10.1063/1.448622  0.673
1985 Pettitt BM, Karplus M. Role of electrostatics in the structure, energy and dynamics of biomolecules: a model study of N-methylalanylacetamide Journal of the American Chemical Society. 107: 1166-1173. DOI: 10.1021/Ja00291A014  0.655
1985 Hemley RJ, Dinur U, Vaida V, Karplus M. Theoretical study of the ground and excited singlet states of styrene Journal of the American Chemical Society. 107: 836-844. DOI: 10.1021/Ja00290A018  0.665
1985 Montgomery Pettitt B, Karplus M. The potential of mean force surface for the alanine dipeptide in aqueous solution: a theoretical approach Chemical Physics Letters. 121: 194-201. DOI: 10.1016/0009-2614(85)85509-3  0.327
1985 Brady J, Karplus M. Configuration entropy of the alanine dipeptide in vacuum and in solution: a molecular dynamics study Journal of the American Chemical Society. 107: 6103-6105. DOI: 10.1002/Chin.198605079  0.325
1985 PETTITT BM, KARPLUS M. ChemInform Abstract: ROLE OF ELECTROSTATICS IN THE STRUCTURE, ENERGY AND DYNAMICS OF BIOMOLECULES: A MODEL STUDY OF N-METHYLALANYLACETAMIDE Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198529077  0.623
1984 Gelin BR, Lee AW, Karplus M. Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism. Journal of Molecular Biology. 171: 489-559. PMID 6663623 DOI: 10.1016/0022-2836(83)90042-6  0.331
1984 Lee AW, Karplus M. Structure-specific model of hemoglobin cooperativity. Proceedings of the National Academy of Sciences of the United States of America. 80: 7055-9. PMID 6580628 DOI: 10.1073/Pnas.80.23.7055  0.336
1984 Novotný J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. Journal of Molecular Biology. 177: 787-818. PMID 6434748 DOI: 10.1016/0022-2836(84)90049-4  0.396
1984 Bashford D, Weaver DL, Karplus M. Diffusion-collision model for the folding kinetics of the lambda-repressor operator-binding domain. Journal of Biomolecular Structure & Dynamics. 1: 1243-55. PMID 6400820 DOI: 10.1080/07391102.1984.10507515  0.592
1984 States DJ, Dobson CM, Karplus M. A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor. Journal of Molecular Biology. 174: 411-8. PMID 6201619 DOI: 10.1016/0022-2836(84)90345-0  0.661
1984 Bashford D, Weaver DL, Lee S, Karplus M. Dynamics of protein folding Acta Crystallographica Section a Foundations of Crystallography. 40: C21-C22. DOI: 10.1107/S0108767384099165  0.718
1984 Coalson RD, Karplus M. New sum rules for electronic absorption spectra The Journal of Chemical Physics. 81: 2891-2896. DOI: 10.1063/1.448063  0.552
1984 Lee S, Karplus M. Brownian dynamics simulations: Statistical error of correlation functions The Journal of Chemical Physics. 81: 6106-6118. DOI: 10.1063/1.447563  0.608
1984 Kohler BE, Spiglanin TA, Hemley RJ, Karplus M. Vibrational analysis of the lowest 1B+u state of trans,trans 1,3,5,7‐octatetraenea) The Journal of Chemical Physics. 80: 23-30. DOI: 10.1063/1.446484  0.589
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