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Arieh Warshel - Publications

Affiliations: 
University of Southern California, Los Angeles, CA, United States 
Area:
Theoretical Chemistry and Biophysics
Website:
http://chem.usc.edu/faculty/Warshel.html
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349 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Xie WJ, Liu D, Wang X, Zhang A, Wei Q, Nandi A, Dong S, Warshel A. Enhancing luciferase activity and stability through generative modeling of natural enzyme sequences. Proceedings of the National Academy of Sciences of the United States of America. 120: e2312848120. PMID 37983512 DOI: 10.1073/pnas.2312848120  0.799
2023 Xie WJ, Liu D, Wang X, Zhang A, Wei Q, Nandi A, Dong S, Warshel A. Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences. Biorxiv : the Preprint Server For Biology. PMID 37786693 DOI: 10.1101/2023.09.18.558367  0.8
2022 Asadi M, Warshel A. Analyzing the Reaction of Orotidine 5'-Phosphate Decarboxylase as a Way to Examine Some Key Catalytic Proposals. Journal of the American Chemical Society. 145: 1334-1341. PMID 36579957 DOI: 10.1021/jacs.2c11728  0.738
2022 Asadi M, Xie WJ, Warshel A. Exploring the Role of Chemical Reactions in the Selectivity of Tyrosine Kinase Inhibitors. Journal of the American Chemical Society. PMID 36044733 DOI: 10.1021/jacs.2c07307  0.691
2022 Xie WJ, Asadi M, Warshel A. Enhancing computational enzyme design by a maximum entropy strategy. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35135886 DOI: 10.1073/pnas.2122355119  0.699
2022 Asadi M, Oanca G, Warshel A. Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. Journal of the American Chemical Society. PMID 35023734 DOI: 10.1021/jacs.1c10494  0.72
2020 Oanca G, Asadi M, Saha A, Ramachandran B, Warshel A. Exploring the Catalytic Reaction of Cysteine Proteases. The Journal of Physical Chemistry. B. PMID 33264018 DOI: 10.1021/acs.jpcb.0c08192  0.717
2020 Bai C, Asadi M, Warshel A. The catalytic dwell in ATPases is not crucial for movement against applied torque. Nature Chemistry. PMID 32958886 DOI: 10.1038/S41557-020-0549-6  0.733
2020 Bai C, Warshel A. Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV. The Journal of Physical Chemistry. B. PMID 32551652 DOI: 10.1021/Acs.Jpcb.0C04317  0.325
2020 Saha A, Oanca G, Mondal D, Warshel A. Exploring the Proteolysis Mechanism of the Proteasomes. The Journal of Physical Chemistry. B. PMID 32498514 DOI: 10.1021/Acs.Jpcb.0C04435  0.387
2020 Mondal D, Kolev V, Warshel A. Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design Acs Catalysis. 10: 6002-6012. DOI: 10.1021/Acscatal.0C01206  0.342
2019 Mondal D, Florian J, Warshel A. Exploring the Effectiveness of Binding Free Energy Calculations. The Journal of Physical Chemistry. B. PMID 31560539 DOI: 10.1021/Acs.Jpcb.9B07593  0.379
2019 Bai C, Warshel A. Revisiting the protomotive vectorial motion of F-ATPase. Proceedings of the National Academy of Sciences of the United States of America. PMID 31511421 DOI: 10.1073/Pnas.1909032116  0.352
2019 Zhao LN, Mondal D, Warshel A. Exploring alternative catalytic mechanisms of Cas9 HNH domain. Proteins. PMID 31390092 DOI: 10.1002/Prot.25796  0.358
2019 Alhadeff R, Warshel A. A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R. Proteins. PMID 31294890 DOI: 10.1002/Prot.25777  0.325
2019 Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z, Warshel A. Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. Proceedings of the National Academy of Sciences of the United States of America. 116: 389-394. PMID 30587585 DOI: 10.1073/Pnas.1804979115  0.715
2019 Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII Acs Catalysis. 9: 1329-1336. DOI: 10.1021/Acscatal.8B04324  0.379
2018 Golan Y, Alhadeff R, Glaser F, Ganoth A, Warshel A, Assaraf YG. Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter. Plos Computational Biology. 14: e1006503. PMID 30388104 DOI: 10.1371/Journal.Pcbi.1006503  0.324
2018 Alhadeff R, Vorobyov I, Yoon HW, Warshel A. Exploring the free-energy landscape of GPCR activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30257944 DOI: 10.1073/Pnas.1810316115  0.762
2018 Lee M, Bai C, Feliks M, Alhadeff R, Warshel A. On the control of the proton current in the voltage-gated proton channel Hv1. Proceedings of the National Academy of Sciences of the United States of America. PMID 30254162 DOI: 10.1073/Pnas.1809766115  0.339
2018 Mondal D, Warshel A. EF-Tu and EF-G are activated by allosteric effects. Proceedings of the National Academy of Sciences of the United States of America. PMID 29531062 DOI: 10.1073/Pnas.1800054115  0.377
2017 Lee M, Kolev V, Warshel A. Validating Coarse Grained Voltage Activation Model by Comparing the Performance to the Results of MC Simulations. The Journal of Physical Chemistry. B. PMID 29156125 DOI: 10.1021/Acs.Jpcb.7B09530  0.37
2017 Jindal G, Ramachandran B, Bora RP, Warshel A. Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases. Acs Catalysis. 7: 3301-3305. PMID 29082065 DOI: 10.1021/Acscatal.7B00171  0.727
2017 Yoon H, Kolev V, Warshel A. Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. The Journal of Physical Chemistry. B. PMID 28911225 DOI: 10.1021/Acs.Jpcb.7B07726  0.361
2017 Garima J, Warshel A. Misunderstanding the Preorganization Concept can lead to Confusions about the Origin of Enzyme Catalysis. Proteins. PMID 28905418 DOI: 10.1002/Prot.25381  0.399
2017 Alhadeff R, Warshel A. Reexamining the origin of the directionality of myosin V. Proceedings of the National Academy of Sciences of the United States of America. PMID 28894003 DOI: 10.1073/Pnas.1711214114  0.378
2017 Mukherjee S, Warshel A. The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function. Photosynthesis Research. PMID 28674936 DOI: 10.1007/S11120-017-0411-X  0.323
2017 Jindal G, Mondal D, Warshel A. Exploring the Drug Resistance of HCV Protease. The Journal of Physical Chemistry. B. PMID 28635289 DOI: 10.1021/Acs.Jpcb.7B04562  0.717
2017 Roy S, Schopf P, Warshel A. On the Origin of Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. The Journal of Physical Chemistry. B. PMID 28613876 DOI: 10.1021/Acs.Jpcb.7B03698  0.381
2017 Yoon H, Warshel A. Simulating the Fidelity And The Three Mg Mechanism of Pol η and clarifying the validity of transition state theory in enzyme catalysis. Proteins. PMID 28383109 DOI: 10.1002/Prot.25305  0.328
2017 Mukherjee S, Alhadeff R, Warshel A. Simulating the dynamics of the mechanochemical cycle of myosin-V. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193897 DOI: 10.1073/Pnas.1700318114  0.335
2016 Alhadeff R, Warshel A. Simulating the Function of the MjNhaP1 Transporter. The Journal of Physical Chemistry. B. PMID 27654405 DOI: 10.1021/Acs.Jpcb.6B08126  0.379
2016 Jindal G, Warshel A. Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region. The Journal of Physical Chemistry. B. PMID 27552257 DOI: 10.1021/Acs.Jpcb.6B07203  0.737
2016 Matute RA, Yoon H, Warshel A. Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β. Proteins. PMID 27488241 DOI: 10.1002/Prot.25106  0.746
2016 Kim I, Warshel A. Analyzing the electrogenicity of cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. PMID 27357681 DOI: 10.1073/Pnas.1608118113  0.599
2016 Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. The Journal of Chemical Physics. 144: 180901. PMID 27179464 DOI: 10.1063/1.4947037  0.367
2016 Astumian RD, Mukherjee S, Warshel A. The Physics and Physical Chemistry of Molecular Machines. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 27149926 DOI: 10.1002/Cphc.201600184  0.316
2016 Lameira JS, Kupchencko I, Warshel A. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. The Journal of Physical Chemistry. B. PMID 26866994 DOI: 10.1021/Acs.Jpcb.5B11966  0.343
2016 Kim I, Warshel A. Equilibrium Fluctuation Relations for Gating Charge in Voltage Sensitive Membrane Proteins: A Microscopic Capacitor Model Approach Biophysical Journal. 110: 105a-106a. DOI: 10.1016/J.Bpj.2015.11.626  0.6
2016 Mukherjee S, Warshel A. Role of the Central Stalk in the Rotary-Chemical Coupling and Torque Generation of F1-ATPase Biophysical Journal. 110: 52a. DOI: 10.1016/J.Bpj.2015.11.345  0.373
2016 Kim I, Warshel A. The Mechanical Insights into Proton/Electron Transfer in Cytochrome C Oxidase Revealed by Direct Modeling of Voltage Changes in Response to Charge Separation Biophysical Journal. 110: 625a. DOI: 10.1016/J.Bpj.2015.11.3352  0.593
2016 Matute RA, Warshel A. Computational Study on the Catalytic Effect of the Magnesium Ions in the Mechanism of DNA Polymerases Biophysical Journal. 110: 547a. DOI: 10.1016/J.Bpj.2015.11.2926  0.723
2015 Kim I, Warshel A. A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. The Journal of Physical Chemistry. B. PMID 26716721 DOI: 10.1021/Acs.Jpcb.5B10956  0.586
2015 Mukherjee S, Bora RP, Warshel A. Torque, chemistry and efficiency in molecular motors: a study of the rotary-chemical coupling in F1-ATPase. Quarterly Reviews of Biophysics. 48: 395-403. PMID 26537397 DOI: 10.1017/S0033583515000050  0.355
2015 Vorobyov I, Kim I, Chu ZT, Warshel A. Refining the treatment of membrane proteins by coarse-grained models. Proteins. PMID 26531155 DOI: 10.1002/Prot.24958  0.593
2015 Alhadeff R, Warshel A. Simulating the function of sodium/proton antiporters. Proceedings of the National Academy of Sciences of the United States of America. 112: 12378-83. PMID 26392528 DOI: 10.1073/Pnas.1516881112  0.327
2015 Kim I, Warshel A. Equilibrium fluctuation relations for voltage coupling in membrane proteins. Biochimica Et Biophysica Acta. 1848: 2985-2997. PMID 26290960 DOI: 10.1016/J.Bbamem.2015.08.008  0.633
2015 Schopf P, Mills MJ, Warshel A. The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm. Proceedings of the National Academy of Sciences of the United States of America. 112: 4328-33. PMID 25805820 DOI: 10.1073/Pnas.1503828112  0.61
2015 Mukherjee S, Warshel A. Dissecting the role of the γ-subunit in the rotary-chemical coupling and torque generation of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 112: 2746-51. PMID 25730883 DOI: 10.1073/Pnas.1500979112  0.37
2015 Bora RP, Mills MJ, Frushicheva MP, Warshel A. On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations. The Journal of Physical Chemistry. B. 119: 3434-45. PMID 25620270 DOI: 10.1021/Jp5124025  0.822
2015 Lameira J, Bora RP, Chu ZT, Warshel A. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins. 83: 318-30. PMID 25388538 DOI: 10.1002/Prot.24717  0.369
2014 Singh MK, Chu ZT, Warshel A. Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters. The Journal of Physical Chemistry. B. 118: 12146-52. PMID 25233046 DOI: 10.1021/Jp507592G  0.373
2014 Warshel A. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). Angewandte Chemie (International Ed. in English). 53: 10020-31. PMID 25060243 DOI: 10.1002/Anie.201403689  0.369
2014 Vicatos S, Rychkova A, Mukherjee S, Warshel A. An effective coarse-grained model for biological simulations: recent refinements and validations. Proteins. 82: 1168-85. PMID 25050439 DOI: 10.1002/Prot.24482  0.816
2014 Kim I, Chakrabarty S, Brzezinski P, Warshel A. Modeling gating charge and voltage changes in response to charge separation in membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 111: 11353-8. PMID 25049404 DOI: 10.1073/Pnas.1411573111  0.681
2014 Mukherjee S, Warshel A. Response to Vilfan: Constructing structure-based free energy surfaces is the key to understand myosin V unidirectionality. Proceedings of the National Academy of Sciences of the United States of America. 111: E2077. PMID 24967456 DOI: 10.1073/Pnas.1404542111  0.353
2014 Frushicheva MP, Mills MJ, Schopf P, Singh MK, Prasad RB, Warshel A. Computer aided enzyme design and catalytic concepts. Current Opinion in Chemical Biology. 21: 56-62. PMID 24814389 DOI: 10.1016/J.Cbpa.2014.03.022  0.802
2014 Kim I, Warshel A. Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel. Proceedings of the National Academy of Sciences of the United States of America. 111: 2128-33. PMID 24464485 DOI: 10.1073/Pnas.1324014111  0.597
2014 Schopf P, Warshel A. Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B. Proteins. 82: 1387-99. PMID 24403025 DOI: 10.1002/Prot.24506  0.357
2014 Kim I, Warshel A. A Structure Based Course-Graining Physical Modeling of the Voltage Activated Kv1.2 Channel - Simulating and Analyzing the Fast Gating Current Biophysical Journal. 106: 743a. DOI: 10.1016/J.Bpj.2013.11.4093  0.596
2014 Mukherjee S, Warshel A. Electrostatic Basis of the Unidirectional Walking Motion in Myosin Molecular Motors Biophysical Journal. 106: 25a-26a. DOI: 10.1016/J.Bpj.2013.11.195  0.361
2013 B RP, Plotnikov NV, Lameira J, Warshel A. Quantitative exploration of the molecular origin of the activation of GTPase. Proceedings of the National Academy of Sciences of the United States of America. 110: 20509-14. PMID 24282301 DOI: 10.1073/Pnas.1319854110  0.771
2013 Mukherjee S, Warshel A. Electrostatic origin of the unidirectionality of walking myosin V motors. Proceedings of the National Academy of Sciences of the United States of America. 110: 17326-31. PMID 24106304 DOI: 10.1073/Pnas.1317641110  0.379
2013 Rychkova A, Warshel A. On the nature of the apparent free energy of inserting amino acids into membrane through the translocon. The Journal of Physical Chemistry. B. 117: 13748-54. PMID 24087983 DOI: 10.1021/Jp406925Y  0.803
2013 Rychkova A, Mukherjee S, Bora RP, Warshel A. Simulating the pulling of stalled elongated peptide from the ribosome by the translocon. Proceedings of the National Academy of Sciences of the United States of America. 110: 10195-200. PMID 23729811 DOI: 10.1016/J.Bpj.2013.11.2749  0.792
2013 Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A. Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. The Journal of Physical Chemistry. B. 117: 12807-19. PMID 23601038 DOI: 10.1021/Jp4020146  0.809
2013 Kamerlin SC, Sharma PK, Prasad RB, Warshel A. Why nature really chose phosphate. Quarterly Reviews of Biophysics. 46: 1-132. PMID 23318152 DOI: 10.1017/S0033583512000157  0.765
2013 Rychkova A, Warshel A. Exploring the nature of the translocon-assisted protein insertion. Proceedings of the National Academy of Sciences of the United States of America. 110: 495-500. PMID 23269832 DOI: 10.1073/Pnas.1220361110  0.821
2013 Prasad BR, Plotnikov NV, Warshel A. Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping. The Journal of Physical Chemistry. B. 117: 153-63. PMID 23198768 DOI: 10.1021/Jp309778N  0.772
2013 Chakrabarty S, Warshel A. Capturing the energetics of water insertion in biological systems: the water flooding approach. Proteins. 81: 93-106. PMID 22911614 DOI: 10.1002/Prot.24165  0.581
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  0.5
2012 Rosta E, Warshel A. On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions. Journal of Chemical Theory and Computation. 8: 3574-3585. PMID 23329895 DOI: 10.1021/Ct2009329  0.659
2012 Frushicheva MP, Mukherjee S, Warshel A. Electrostatic origin of the catalytic effect of a supramolecular host catalyst. The Journal of Physical Chemistry. B. 116: 13353-60. PMID 23088306 DOI: 10.1021/Jp3084327  0.768
2012 Klvaňa M, Murphy DL, Jeřábek P, Goodman MF, Warshel A, Sweasy JB, Florián J. Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment. Biochemistry. 51: 8829-43. PMID 23013478 DOI: 10.1021/Bi300783T  0.359
2012 Mukherjee S, Warshel A. Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 109: 14876-81. PMID 22927379 DOI: 10.1073/Pnas.1212841109  0.355
2012 Plotnikov NV, Warshel A. Exploring, refining, and validating the paradynamics QM/MM sampling. The Journal of Physical Chemistry. B. 116: 10342-56. PMID 22853800 DOI: 10.1021/Jp304678D  0.748
2012 Dryga A, Chakrabarty S, Vicatos S, Warshel A. Realistic simulation of the activation of voltage-gated ion channels. Proceedings of the National Academy of Sciences of the United States of America. 109: 3335-40. PMID 22331900 DOI: 10.1073/Pnas.1121094109  0.797
2012 Singh N, Frushicheva MP, Warshel A. Validating the vitality strategy for fighting drug resistance. Proteins. 80: 1110-22. PMID 22275047 DOI: 10.1002/Prot.24012  0.752
2012 Frushicheva MP, Warshel A. Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A. Chembiochem : a European Journal of Chemical Biology. 13: 215-23. PMID 22190449 DOI: 10.1002/Cbic.201100600  0.772
2012 Dryga A, Chakrabarty S, Vicatos S, Warshel A. Coarse grained model for exploring voltage dependent ion channels. Biochimica Et Biophysica Acta. 1818: 303-17. PMID 21843502 DOI: 10.1016/J.Bbamem.2011.07.043  0.796
2012 Warshel A, Mukherjee S. Realistic Modeling of Biological Motors; Electrostatic Origin of the Mechnochemical Rotatory Mechanism and the Catalytic Dwell of F1-ATPase Biophysical Journal. 102: 712a. DOI: 10.1016/J.Bpj.2011.11.3863  0.436
2012 Rychkova A, Warshel A. Computational Approach to Study Membrane Protein Topology Biophysical Journal. 102: 624a. DOI: 10.1016/J.Bpj.2011.11.3400  0.799
2012 Mukherjee S, Warshel A. Role of Electrostatics in the Mechanochemical Rotary Mechanism of F1-ATPase Biophysical Journal. 102: 225a. DOI: 10.1016/J.Bpj.2011.11.1236  0.346
2012 Prasad BR, Kamerlin SCL, Florián J, Warshel A. Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting Theoretical Chemistry Accounts. 131: 1-15. DOI: 10.1007/S00214-012-1288-6  0.401
2011 Mukherjee S, Warshel A. Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 108: 20550-5. PMID 22143769 DOI: 10.1073/Pnas.1117024108  0.424
2011 Warshel A, Dryga A. Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties. Proteins. 79: 3469-84. PMID 21910139 DOI: 10.1002/Prot.23125  0.792
2011 Ram Prasad B, Warshel A. Prechemistry versus preorganization in DNA replication fidelity. Proteins. 79: 2900-19. PMID 21905114 DOI: 10.1002/Prot.23128  0.39
2011 Adamczyk AJ, Cao J, Kamerlin SC, Warshel A. Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proceedings of the National Academy of Sciences of the United States of America. 108: 14115-20. PMID 21831831 DOI: 10.1073/Pnas.1111252108  0.802
2011 Plotnikov NV, Kamerlin SC, Warshel A. Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks. The Journal of Physical Chemistry. B. 115: 7950-62. PMID 21618985 DOI: 10.1021/Jp201217B  0.814
2011 Adamczyk AJ, Warshel A. Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proceedings of the National Academy of Sciences of the United States of America. 108: 9827-32. PMID 21617092 DOI: 10.1073/Pnas.1105714108  0.742
2011 Kamerlin SC, Warshel A. Multiscale modeling of biological functions. Physical Chemistry Chemical Physics : Pccp. 13: 10401-11. PMID 21526232 DOI: 10.1039/C0Cp02823A  0.667
2011 Johansson AL, Chakrabarty S, Berthold CL, Högbom M, Warshel A, Brzezinski P. Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects. Biochimica Et Biophysica Acta. 1807: 1083-94. PMID 21463601 DOI: 10.1016/J.Bbabio.2011.03.012  0.562
2011 Frushicheva MP, Cao J, Warshel A. Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. Biochemistry. 50: 3849-58. PMID 21443179 DOI: 10.1021/Bi200063A  0.805
2011 Chakrabarty S, Namslauer I, Brzezinski P, Warshel A. Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. Biochimica Et Biophysica Acta. 1807: 413-26. PMID 21232525 DOI: 10.1016/J.Bbabio.2011.01.004  0.583
2011 Kamerlin SC, Vicatos S, Dryga A, Warshel A. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annual Review of Physical Chemistry. 62: 41-64. PMID 21034218 DOI: 10.1146/Annurev-Physchem-032210-103335  0.796
2011 Rychkova A, Warshel A. Computational Studies of Translocon-Assisted Processes of Membrane Protein Insertion and Translocation Biophysical Journal. 100: 544a. DOI: 10.1016/J.Bpj.2010.12.3172  0.795
2011 Cao J, Warshel A. A Comprehensive Examination of the Contributions to Binding and Activation Entropies Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3135  0.546
2011 Dryga A, Warshel A. External Electric Field in the Atomistic Simulation of Membrane Systems Biophysical Journal. 100: 333a. DOI: 10.1016/J.Bpj.2010.12.2023  0.75
2011 Frushicheva MP, Warshel A. Computational Enzyme Design: Refining Artificial Enzymes and Exploring Paths of Directed Evolution Biophysical Journal. 100: 219a. DOI: 10.1016/J.Bpj.2010.12.1407  0.792
2011 Kamerlin SCL, Warshel A. The empirical valence bond model: Theory and applications Wiley Interdisciplinary Reviews: Computational Molecular Science. 1: 30-45. DOI: 10.1002/Wcms.10  0.41
2010 Kamerlin SC, Warshel A. The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions. Faraday Discussions. 145: 71-106. PMID 25285029 DOI: 10.1039/B907354J  0.707
2010 Kamerlin SC, Warshel A. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. Journal of Physical Organic Chemistry. 23: 677-684. PMID 21494414 DOI: 10.1002/Poc.1620  0.737
2010 Rychkova A, Vicatos S, Warshel A. On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes. Proceedings of the National Academy of Sciences of the United States of America. 107: 17598-603. PMID 20876127 DOI: 10.1073/Pnas.1012207107  0.811
2010 Dryga A, Warshel A. Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules. The Journal of Physical Chemistry. B. 114: 12720-8. PMID 20836533 DOI: 10.1021/Jp1056122  0.762
2010 Frushicheva MP, Cao J, Chu ZT, Warshel A. Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proceedings of the National Academy of Sciences of the United States of America. 107: 16869-74. PMID 20829491 DOI: 10.1073/Pnas.1010381107  0.802
2010 Kamerlin SC, Chu ZT, Warshel A. On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models. The Journal of Organic Chemistry. 75: 6391-401. PMID 20825150 DOI: 10.1021/Jo100651S  0.712
2010 Kamerlin SC, Mavri J, Warshel A. Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. Febs Letters. 584: 2759-66. PMID 20433839 DOI: 10.1016/J.Febslet.2010.04.062  0.665
2010 Singh N, Warshel A. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins. 78: 1705-23. PMID 20186976 DOI: 10.1002/Prot.22687  0.382
2010 Singh N, Warshel A. A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. Proteins. 78: 1724-35. PMID 20186973 DOI: 10.1002/Prot.22689  0.401
2010 Kamerlin SC, Sharma PK, Chu ZT, Warshel A. Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization. Proceedings of the National Academy of Sciences of the United States of America. 107: 4075-80. PMID 20150513 DOI: 10.1073/Pnas.0914579107  0.767
2010 Kamerlin SC, Warshel A. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins. 78: 1339-75. PMID 20099310 DOI: 10.1002/Prot.22654  0.715
2010 Messer BM, Roca M, Chu ZT, Vicatos S, Kilshtain AV, Warshel A. Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins. 78: 1212-27. PMID 20052756 DOI: 10.1002/Prot.22640  0.465
2010 Rucker R, Oelschlaeger P, Warshel A. A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases. Proteins. 78: 671-80. PMID 19842163 DOI: 10.1002/Prot.22596  0.327
2010 Warshel A, Schlosser DW. Electrostatic control of the efficiency of light-induced electron transfer across membranes. Proceedings of the National Academy of Sciences of the United States of America. 78: 5564-8. PMID 16593088 DOI: 10.1073/Pnas.78.9.5564  0.358
2010 Warshel A. Role of the chlorophyll dimer in bacterial photosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 77: 3105-9. PMID 16592832 DOI: 10.1073/Pnas.77.6.3105  0.309
2010 Kamerlin SCL, Warshel A. Reply to Karplus: Conformational dynamics have no role in the chemical step Proceedings of the National Academy of Sciences of the United States of America. 107: E72. DOI: 10.1073/Pnas.1002658107  0.326
2010 Alkherraz A, Kamerlin SCL, Feng G, Sheikh QI, Warshel A, Williams NH. Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer Faraday Discussions. 145: 281-299. DOI: 10.1039/B908398G  0.379
2010 Frushicheva MP, Warshel A. Electrostatic Contribution to the Transition States Binding Free Energy Using Simplified Coarse Grained Model Biophysical Journal. 98: 44a. DOI: 10.1016/J.Bpj.2009.12.252  0.792
2009 Kamerlin SC, Warshel A. On the energetics of ATP hydrolysis in solution. The Journal of Physical Chemistry. B. 113: 15692-8. PMID 19888735 DOI: 10.1021/Jp907223T  0.692
2009 Vicatos S, Roca M, Warshel A. Effective approach for calculations of absolute stability of proteins using focused dielectric constants. Proteins. 77: 670-84. PMID 19856460 DOI: 10.1002/Prot.22481  0.379
2009 Pisliakov AV, Cao J, Kamerlin SC, Warshel A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proceedings of the National Academy of Sciences of the United States of America. 106: 17359-64. PMID 19805169 DOI: 10.1073/Pnas.0909150106  0.725
2009 Kamerlin SC, Cao J, Rosta E, Warshel A. On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. The Journal of Physical Chemistry. B. 113: 10905-15. PMID 19606825 DOI: 10.1021/Jp901709F  0.769
2009 Kilshtain AV, Warshel A. On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes. Proteins. 77: 536-50. PMID 19480013 DOI: 10.1002/Prot.22466  0.431
2009 Singh N, Warshel A. Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects. The Journal of Physical Chemistry. B. 113: 7372-82. PMID 19402609 DOI: 10.1021/Jp811063V  0.432
2009 Kamerlin SC, McKenna CE, Goodman MF, Goondman MF, Warshel A. A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. Biochemistry. 48: 5963-71. PMID 19391628 DOI: 10.1021/Bi900140C  0.696
2009 Liu H, Shi Y, Chen XS, Warshel A. Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases. Proceedings of the National Academy of Sciences of the United States of America. 106: 7449-54. PMID 19383795 DOI: 10.1073/Pnas.0900532106  0.371
2009 Kamerlin SC, Haranczyk M, Warshel A. Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 10: 1125-34. PMID 19301306 DOI: 10.1002/Cphc.200800753  0.697
2009 Vardi-Kilshtain A, Roca M, Warshel A. The empirical valence bond as an effective strategy for computer-aided enzyme design. Biotechnology Journal. 4: 495-500. PMID 19229886 DOI: 10.1002/Biot.200800299  0.356
2009 Roca M, Vardi-Kilshtain A, Warshel A. Toward accurate screening in computer-aided enzyme design. Biochemistry. 48: 3046-56. PMID 19161327 DOI: 10.1021/Bi802191B  0.41
2009 Kamerlin SC, Haranczyk M, Warshel A. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. The Journal of Physical Chemistry. B. 113: 1253-72. PMID 19055405 DOI: 10.1021/Jp8071712  0.741
2008 Roca M, Messer B, Hilvert D, Warshel A. On the relationship between folding and chemical landscapes in enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. 105: 13877-82. PMID 18779576 DOI: 10.1073/Pnas.0803405105  0.441
2008 Kamerlin SC, Williams NH, Warshel A. Dineopentyl phosphate hydrolysis: evidence for stepwise water attack. The Journal of Organic Chemistry. 73: 6960-9. PMID 18729515 DOI: 10.1021/Jo801207Q  0.702
2008 Kamerlin SC, Florián J, Warshel A. Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 9: 1767-73. PMID 18666265 DOI: 10.1002/Cphc.200800356  0.699
2008 Haranczyk M, Gutowski M, Warshel A. Solvation free energies of molecules. The most stable anionic tautomers of uracil. Physical Chemistry Chemical Physics : Pccp. 10: 4442-8. PMID 18654684 DOI: 10.1039/B802300J  0.426
2008 Pisliakov AV, Sharma PK, Chu ZT, Haranczyk M, Warshel A. Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. 105: 7726-31. PMID 18509049 DOI: 10.1073/Pnas.0800580105  0.591
2008 Rosta E, Haranczyk M, Chu ZT, Warshel A. Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. The Journal of Physical Chemistry. B. 112: 5680-92. PMID 18412414 DOI: 10.1021/Jp711496Y  0.693
2008 Braun-Sand S, Sharma PK, Chu ZT, Pisliakov AV, Warshel A. The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochimica Et Biophysica Acta. 1777: 441-52. PMID 18387356 DOI: 10.1016/J.Bbabio.2008.03.001  0.6
2008 Rosta E, Kamerlin SC, Warshel A. On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. Biochemistry. 47: 3725-35. PMID 18307312 DOI: 10.1021/Bi702106M  0.789
2008 Xiang Y, Warshel A. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping. The Journal of Physical Chemistry. B. 112: 1007-15. PMID 18166038 DOI: 10.1021/Jp076931F  0.449
2008 Sucato CA, Upton TG, Kashemirov BA, Osuna J, Oertell K, Beard WA, Wilson SH, Florián J, Warshel A, McKenna CE, Goodman MF. DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry. 47: 870-9. PMID 18161950 DOI: 10.1021/Bi7014162  0.355
2008 Mavri J, Liu H, Olsson MH, Warshel A. Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase. The Journal of Physical Chemistry. B. 112: 5950-4. PMID 18069813 DOI: 10.1021/Jp0758420  0.396
2008 Xiang Y, Goodman MF, Beard WA, Wilson SH, Warshel A. Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins. 70: 231-47. PMID 17671961 DOI: 10.1002/Prot.21668  0.352
2007 Warshel A, Kato M, Pisliakov AV. Polarizable Force Fields:  History, Test Cases, and Prospects. Journal of Chemical Theory and Computation. 3: 2034-45. PMID 26636199 DOI: 10.1021/Ct700127W  0.51
2007 Roca M, Liu H, Messer B, Warshel A. On the relationship between thermal stability and catalytic power of enzymes. Biochemistry. 46: 15076-88. PMID 18052079 DOI: 10.1021/Bi701732A  0.386
2007 Liu H, Warshel A. Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. The Journal of Physical Chemistry. B. 111: 7852-61. PMID 17571875 DOI: 10.1021/Jp070938F  0.362
2007 Sharma PK, Chu ZT, Olsson MH, Warshel A. A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proceedings of the National Academy of Sciences of the United States of America. 104: 9661-6. PMID 17517615 DOI: 10.1073/Pnas.0702238104  0.604
2007 Liu H, Warshel A. The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry. 46: 6011-25. PMID 17469852 DOI: 10.1021/Bi700201W  0.393
2007 Roca M, Messer B, Warshel A. Electrostatic contributions to protein stability and folding energy. Febs Letters. 581: 2065-71. PMID 17466986 DOI: 10.1016/J.Febslet.2007.04.025  0.405
2007 Olsson MH, Siegbahn PE, Blomberg MR, Warshel A. Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. Biochimica Et Biophysica Acta. 1767: 244-60. PMID 17350588 DOI: 10.1016/J.Bbabio.2007.01.015  0.456
2007 Martínek V, Bren U, Goodman MF, Warshel A, Florián J. DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. Febs Letters. 581: 775-80. PMID 17286973 DOI: 10.1016/J.Febslet.2007.01.042  0.314
2007 Warshel A, Sharma PK, Chu ZT, Aqvist J. Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase. Biochemistry. 46: 1466-76. PMID 17279612 DOI: 10.1021/Bi061752U  0.575
2007 Oelschlaeger P, Klahn M, Beard WA, Wilson SH, Warshel A. Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects. Journal of Molecular Biology. 366: 687-701. PMID 17174326 DOI: 10.1016/J.Jmb.2006.10.095  0.346
2007 Warshel A, Kato M, Pisliakov AV. Polarizable force fields: History, test cases, and prospects Journal of Chemical Theory and Computation. 3: 2034-2045. DOI: 10.1021/ct700127w  0.366
2007 Kato M, Braun-Sand S, Warshel A. Challenges and progresses in calculations of binding free energies-what does it take to quantify electrostatic contributions to protein-ligand interactions? Rsc Biomolecular Sciences. 268-290.  0.48
2006 Klähn M, Rosta E, Warshel A. On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins. Journal of the American Chemical Society. 128: 15310-23. PMID 17117884 DOI: 10.1021/Ja065470T  0.687
2006 Warshel A, Sharma PK, Kato M, Parson WW. Modeling electrostatic effects in proteins. Biochimica Et Biophysica Acta. 1764: 1647-76. PMID 17049320 DOI: 10.1016/J.Bbapap.2006.08.007  0.7
2006 Hong G, Rosta E, Warshel A. Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. The Journal of Physical Chemistry. B. 110: 19570-4. PMID 17004821 DOI: 10.1021/Jp0625199  0.647
2006 Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJ, Besley NA, ... ... Warshel A, et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics : Pccp. 8: 3172-91. PMID 16902710 DOI: 10.1039/B517914A  0.629
2006 Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH. Electrostatic basis for enzyme catalysis. Chemical Reviews. 106: 3210-35. PMID 16895325 DOI: 10.1021/Cr0503106  0.643
2006 Olsson MH, Mavri J, Warshel A. Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1417-32. PMID 16873128 DOI: 10.1098/Rstb.2006.1880  0.449
2006 Kato M, Pisliakov AV, Warshel A. The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins. 64: 829-44. PMID 16779836 DOI: 10.1002/Prot.21012  0.596
2006 Kato M, Warshel A. Using a charging coordinate in studies of ionization induced partial unfolding. The Journal of Physical Chemistry. B. 110: 11566-70. PMID 16771433 DOI: 10.1021/Jp061190O  0.578
2006 Xiang Y, Oelschlaeger P, Florián J, Goodman MF, Warshel A. Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta. Biochemistry. 45: 7036-48. PMID 16752894 DOI: 10.1021/Bi060147O  0.412
2006 Olsson MH, Warshel A. Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. 103: 6500-5. PMID 16614069 DOI: 10.1073/Pnas.0510860103  0.342
2006 Rosta E, Klähn M, Warshel A. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. The Journal of Physical Chemistry. B. 110: 2934-41. PMID 16471904 DOI: 10.1021/Jp057109J  0.692
2006 Burykin A, Warshel A. Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano-Filtration Devices Journal of Computational and Theoretical Nanoscience. 3: 237-242. DOI: 10.1166/Jctn.2006.3003  0.69
2005 Kato M, Warshel A. Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels. The Journal of Physical Chemistry. B. 109: 19516-22. PMID 16853521 DOI: 10.1021/Jp053208L  0.509
2005 Klähn M, Braun-Sand S, Rosta E, Warshel A. On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. The Journal of Physical Chemistry. B. 109: 15645-50. PMID 16852982 DOI: 10.1021/Jp0521757  0.69
2005 Braun-Sand S, Burykin A, Chu ZT, Warshel A. Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects. The Journal of Physical Chemistry. B. 109: 583-92. PMID 16851050 DOI: 10.1021/Jp0465783  0.737
2005 Sharma PK, Xiang Y, Kato M, Warshel A. What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry. 44: 11307-14. PMID 16114867 DOI: 10.1021/Bi0509806  0.68
2005 Florián J, Goodman MF, Warshel A. Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases. Proceedings of the National Academy of Sciences of the United States of America. 102: 6819-24. PMID 15863620 DOI: 10.1073/Pnas.0408173102  0.392
2005 Olsson MH, Sharma PK, Warshel A. Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck. Febs Letters. 579: 2026-34. PMID 15811313 DOI: 10.1016/J.Febslet.2005.02.051  0.63
2005 Warshel A. Inverting the selectivity of aquaporin 6: gating versus direct electrostatic interaction. Proceedings of the National Academy of Sciences of the United States of America. 102: 1813-4. PMID 15684047 DOI: 10.1073/Pnas.0409788102  0.342
2004 Olsson MH, Warshel A. Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark. Journal of the American Chemical Society. 126: 15167-79. PMID 15548014 DOI: 10.1021/Ja047151C  0.409
2004 Braun-Sand S, Strajbl M, Warshel A. Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models. Biophysical Journal. 87: 2221-39. PMID 15454425 DOI: 10.1529/Biophysj.104.043257  0.458
2004 Burykin A, Warshel A. On the origin of the electrostatic barrier for proton transport in aquaporin. Febs Letters. 570: 41-6. PMID 15251436 DOI: 10.1016/J.Febslet.2004.06.020  0.724
2004 Schutz CN, Warshel A. The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases. Proteins. 55: 711-23. PMID 15103633 DOI: 10.1002/Prot.20096  0.82
2004 Shurki A, Strajbl M, Schutz CN, Warshel A. Electrostatic basis for bioenergetics. Methods in Enzymology. 380: 52-84. PMID 15051332 DOI: 10.1016/S0076-6879(04)80003-X  0.781
2004 Shurki A, Warshel A. Why does the Ras switch "break" by oncogenic mutations? Proteins. 55: 1-10. PMID 14997535 DOI: 10.1002/Prot.20004  0.348
2004 Olsson MH, Siegbahn PE, Warshel A. Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase. Journal of the American Chemical Society. 126: 2820-8. PMID 14995199 DOI: 10.1021/Ja037233L  0.452
2004 Olsson MH, Siegbahn PE, Warshel A. Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 9: 96-9. PMID 14663649 DOI: 10.1007/S00775-003-0503-2  0.384
2004 Parson WW, Warshel A. Dependence of photosynthetic electron-transfer kinetics on temperature and energy in a density-matrix model Journal of Physical Chemistry B. 108: 10474-10483. DOI: 10.1021/Jp0495904  0.333
2004 Schutz CN, Warshel A. Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited Journal of Physical Chemistry B. 108: 2066-2075. DOI: 10.1021/Jp0366015  0.379
2004 Parson WW, Warshel A. A density-matrix model of photosynthetic electron transfer with microscopically estimated vibrational relaxation times Chemical Physics. 296: 201-216. DOI: 10.1016/J.Chemphys.2003.10.006  0.315
2003 Strajbl M, Shurki A, Warshel A. Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase. Proceedings of the National Academy of Sciences of the United States of America. 100: 14834-9. PMID 14657336 DOI: 10.1073/Pnas.2436328100  0.414
2003 Burykin A, Warshel A. What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. Biophysical Journal. 85: 3696-706. PMID 14645061 DOI: 10.1016/S0006-3495(03)74786-9  0.715
2003 Shurki A, Warshel A. Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. Advances in Protein Chemistry. 66: 249-313. PMID 14631821 DOI: 10.1016/S0065-3233(03)66007-9  0.441
2003 Strajbl M, Shurki A, Kato M, Warshel A. Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. Journal of the American Chemical Society. 125: 10228-37. PMID 12926945 DOI: 10.1021/Ja0356481  0.566
2003 Burykin A, Kato M, Warshel A. Exploring the origin of the ion selectivity of the KcsA potassium channel. Proteins. 52: 412-26. PMID 12866052 DOI: 10.1002/Prot.10455  0.753
2003 Florián J, Goodman MF, Warshel A. Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. Journal of the American Chemical Society. 125: 8163-77. PMID 12837086 DOI: 10.1021/Ja028997O  0.418
2003 Olsson MH, Hong G, Warshel A. Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin. Journal of the American Chemical Society. 125: 5025-39. PMID 12708852 DOI: 10.1021/Ja0212157  0.432
2003 Barbany M, Gutiérrez-de-Terán H, Sanz F, Villà-Freixa J, Warshel A. On the generation of catalytic antibodies by transition state analogues. Chembiochem : a European Journal of Chemical Biology. 4: 277-85. PMID 12672107 DOI: 10.1002/Cbic.200390048  0.801
2003 Florián J, Goodman MF, Warshel A. Computer simulation studies of the fidelity of DNA polymerases. Biopolymers. 68: 286-99. PMID 12601790 DOI: 10.1002/Bip.10244  0.313
2003 Warshel A. Computer simulations of enzyme catalysis: methods, progress, and insights. Annual Review of Biophysics and Biomolecular Structure. 32: 425-43. PMID 12574064 DOI: 10.1146/Annurev.Biophys.32.110601.141807  0.434
2002 Warshel A. Molecular dynamics simulations of biological reactions. Accounts of Chemical Research. 35: 385-95. PMID 12069623 DOI: 10.1021/Ar010033Z  0.372
2002 Burykin A, Schutz CN, Villá J, Warshel A. Simulations of ion current in realistic models of ion channels: the KcsA potassium channel. Proteins. 47: 265-80. PMID 11948781 DOI: 10.1002/Prot.10106  0.792
2002 Shurki A, Strajbl M, Villà J, Warshel A. How much do enzymes really gain by restraining their reacting fragments? Journal of the American Chemical Society. 124: 4097-107. PMID 11942849 DOI: 10.1021/ja012230z  0.351
2002 Štrajbl M, Hong G, Warshel A. Ab initio QM/MM simulation with proper sampling: "First principle" calculations of the free energy of the autodissociation of water in aqueous solution Journal of Physical Chemistry B. 106: 13333-13343. DOI: 10.1021/Jp021625H  0.436
2002 Florián J, Goodman MF, Warshel A. Theoretical investigation of the binding free energies and key substrate-recognition components of the replication fidelity of human DNA polymerase β Journal of Physical Chemistry B. 106: 5739-5753. DOI: 10.1021/Jp020790U  0.356
2001 Warshel A, Parson WW. Dynamics of biochemical and biophysical reactions: insight from computer simulations. Quarterly Reviews of Biophysics. 34: 563-679. PMID 11852595 DOI: 10.1017/S0033583501003730  0.443
2001 Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins. 44: 400-17. PMID 11484218 DOI: 10.1002/Prot.1106  0.8
2001 Villà J, Warshel A. Energetics and dynamics of enzymatic reactions Journal of Physical Chemistry B. 105: 7887-7907. DOI: 10.1021/Jp011048H  0.46
2001 Warshel A, Chu ZT. Nature of the surface crossing process in bacteriorhodopsin: Computer simulations of the quantum dynamics of the primary photochemical event Journal of Physical Chemistry B. 105: 9857-9871. DOI: 10.1021/Jp010704A  0.331
2001 Ŝtrajbl M, Florián J, Warshel A. Ab initio evaluation of the free energy surfaces for the general base/acid catalyzed thiolysis of formamide and the hydrolysis of methyl thiolformate: A reference solution reaction for studies of cysteine proteases Journal of Physical Chemistry B. 105: 4471-4484. DOI: 10.1021/Jp010279L  0.4
2000 Warshel A, Strajbl M, Villà J, Florián J. Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. Biochemistry. 39: 14728-38. PMID 11101287 DOI: 10.1021/Bi000987H  0.476
2000 Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A. How important are entropic contributions to enzyme catalysis? Proceedings of the National Academy of Sciences of the United States of America. 97: 11899-904. PMID 11050223 DOI: 10.1073/Pnas.97.22.11899  0.778
2000 Mehler EL, Warshel A. Comment on "a fast and simple method to calculate protonation states in proteins". Proteins. 40: 1-3. PMID 10813824 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<1::Aid-Prot10>3.0.Co;2-O  0.314
2000 Sham YY, Chu ZT, Tao H, Warshel A. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins. 39: 393-407. PMID 10813821 DOI: 10.1002/(Sici)1097-0134(20000601)39:4<393::Aid-Prot120>3.0.Co;2-H  0.774
2000 Florián J, Goodman MF, Warshel A. Free-energy perturbation calculations of DNA destabilization by base substitutions: The effect of neutral guanine·thymine, adenine·cytosine and adenine·difluorotoluene mismatches Journal of Physical Chemistry B. 104: 10092-10099. DOI: 10.1021/Jp001760Z  0.368
2000 Strajbl M, Sham YY, Villà J, Chu ZT, Warshel A. Calculations of Activation Entropies of Chemical Reactions in Solution Journal of Physical Chemistry B. 104: 4578-4584. DOI: 10.1021/Jp0003095  0.773
2000 Várnai P, Warshel A. Computer simulation studies of the catalytic mechanism of human aldose reductase Journal of the American Chemical Society. 122: 3849-3860. DOI: 10.1021/Ja994246J  0.411
2000 Štrajbl M, Florián J, Warshel A. Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases Journal of the American Chemical Society. 122: 5354-5366. DOI: 10.1021/Ja992441S  0.371
2000 Hong G, Strajbl M, Wesolowski TA, Warshel A. Constraining the Electron Densities in DFT Method as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions Journal of Computational Chemistry. 21: 1554-1561. DOI: 10.1002/1096-987X(200012)21:16<1554::Aid-Jcc12>3.0.Co;2-I  0.396
2000 Štrajbl M, Florián J, Warshel A. Ab initio/LD Studies of Chemical Reactions in Solution: Reference Free-Energy Surfaces for Acylation Reactions Occurring in Serine and Cysteine Proteases International Journal of Quantum Chemistry. 77: 44-53. DOI: 10.1002/(Sici)1097-461X(2000)77:1<44::Aid-Qua6>3.0.Co;2-A  0.359
2000 Villà J, Bentzien J, González-Lafont A, Lluch JM, Bertran J, Warshel A. Effective Way of Modeling Chemical Catalysis: Empirical Valence Bond Picture of Role of Solvent and Catalyst in Alkylation Reactions Journal of Computational Chemistry. 21: 607-625. DOI: 10.1002/(Sici)1096-987X(200006)21:8<607::Aid-Jcc3>3.0.Co;2-R  0.382
1999 Sham YY, Muegge I, Warshel A. Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center. Proteins. 36: 484-500. PMID 10450091 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<484::Aid-Prot13>3.0.Co;2-R  0.775
1999 Aqvist J, Kolmodin K, Florian J, Warshel A. Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data? Chemistry & Biology. 6: R71-80. PMID 10074472 DOI: 10.1016/S1074-5521(99)89003-6  0.387
1999 Florián J, Warshel A. Quantum-chemical insights into mechanisms of the nonenzymatic hydrolysis of phosphate monoesters Phosphorus, Sulfur and Silicon and Related Elements. 144: 525-528. DOI: 10.1080/10426509908546297  0.355
1999 Florián J, Warshel A. Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model Journal of Physical Chemistry B. 103: 10282-10288. DOI: 10.1021/Jp992041R  0.388
1999 Jen CF, Warshel A. Microscopic based density matrix treatments of electron-transfer reactions in condensed phases Journal of Physical Chemistry A. 103: 11378-11386. DOI: 10.1021/Jp991304E  0.31
1999 Florián J, Šponer J, Warshel A. Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: Ab initio/langevin dipoles study Journal of Physical Chemistry B. 103: 884-892. DOI: 10.1021/Jp983699S  0.34
1999 Fan ZZ, Hwang J, Warshel A. Using simplified protein representation as a reference potential for all-atom calculations of folding free energy Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 103: 77-80. DOI: 10.1007/S002140050516  0.428
1998 Warshel A. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. The Journal of Biological Chemistry. 273: 27035-8. PMID 9765214 DOI: 10.1074/Jbc.273.42.27035  0.308
1998 Warshel A, Papazyan A. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Current Opinion in Structural Biology. 8: 211-7. PMID 9631295 DOI: 10.1016/S0959-440X(98)80041-9  0.402
1998 Warshel A, Florián J. Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. Proceedings of the National Academy of Sciences of the United States of America. 95: 5950-5. PMID 9600897 DOI: 10.1073/Pnas.95.11.5950  0.448
1998 Sham YY, Muegge I, Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophysical Journal. 74: 1744-53. PMID 9545037 DOI: 10.1016/S0006-3495(98)77885-3  0.765
1998 Muegge I, Schweins T, Warshel A. Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction. Proteins. 30: 407-23. PMID 9533625 DOI: 10.1002/(Sici)1097-0134(19980301)30:4<407::Aid-Prot8>3.0.Co;2-F  0.405
1998 Parson WW, Chu ZT, Warshel A. Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers. Biophysical Journal. 74: 182-91. PMID 9449321 DOI: 10.1016/S0006-3495(98)77778-1  0.388
1998 Sham YY, Warshel A. The surface constraint all atom model provides size independent results in calculations of hydration free energies Journal of Chemical Physics. 109: 7940-7944. DOI: 10.1063/1.477441  0.776
1998 Parson WW, Chu ZT, Warshel A. Oscillations of the energy gap for the initial electron-transfer step in bacterial reaction centers Photosynthesis Research. 55: 147-152. DOI: 10.1023/A:1005992121305  0.309
1998 Bentzien J, Muller RP, Florián J, Warshel A. Hybrid ab initio quantum mechanics/molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin Journal of Physical Chemistry B. 102: 2293-2301. DOI: 10.1021/Jp973480Y  0.425
1998 Florián J, Warshel A. Phosphate ester hydrolysis in aqueous solution: Associative versus dissociative mechanisms Journal of Physical Chemistry B. 102: 719-734. DOI: 10.1021/Jp972182Y  0.331
1998 Florian J, Aqvist J, Warshel A. On the reactivity of phosphate monoester dianions in aqueous solution: Bronsted linear free-energy relationships do not have an unique mechanistic interpretation [8] Journal of the American Chemical Society. 120: 11524-11525. DOI: 10.1021/Ja982698A  0.336
1998 Glennon TM, Warshel A. Energetics of the catalytic reaction of ribonuclease A: A computational study of alternative mechanisms Journal of the American Chemical Society. 120: 10234-10247. DOI: 10.1021/Ja981594X  0.447
1998 Fuxreiter M, Warshel A. Origin of the catalytic power of acetylcholinesterase: Computer simulation studies Journal of the American Chemical Society. 120: 183-194. DOI: 10.1021/Ja972326M  0.438
1997 Muegge I, Tao H, Warshel A. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Protein Engineering. 10: 1363-72. PMID 9542997 DOI: 10.1093/Protein/10.12.1363  0.37
1997 Papazyan A, Warshel A. Continuum and Dipole-Lattice Models of Solvation The Journal of Physical Chemistry B. 101: 11254-11264. DOI: 10.1021/Jp971632J  0.303
1997 Florián J, Warshel A. Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution:  Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution The Journal of Physical Chemistry B. 101: 5583-5595. DOI: 10.1021/Jp9705075  0.362
1997 Sham YY, Chu ZT, Warshel A. Consistent Calculations of pKa's of Ionizable Residues in Proteins:  Semi-microscopic and Microscopic Approaches The Journal of Physical Chemistry B. 101: 4458-4472. DOI: 10.1021/Jp963412W  0.771
1997 Muegge I, Qi PX, Wand AJ, Chu ZT, Warshel A. The Reorganization Energy of Cytochrome c Revisited The Journal of Physical Chemistry. 101: 825-836. DOI: 10.1021/Jp962478O  0.373
1997 Warshel A, Chu Z, Parson W. Two-dimensional free energy surfaces for primary electron transfer in a photosynthetic reaction center Chemical Physics Letters. 265: 293-296. DOI: 10.1016/S0009-2614(96)01415-7  0.38
1997 Warshel A, Papazyan A, Muegge I. Microscopic and semimacroscopic redox calculations: what can and cannot be learned from continuum models Jbic Journal of Biological Inorganic Chemistry. 2: 143-152. DOI: 10.1007/S007750050119  0.391
1996 Muller RP, Warshel A. Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 524-38. PMID 9390256  0.307
1996 Warshel A, Papazyan A. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. Proceedings of the National Academy of Sciences of the United States of America. 93: 13665-70. PMID 8942991 DOI: 10.1073/Pnas.93.24.13665  0.316
1996 Schweins T, Warshel A. Mechanistic analysis of the observed linear free energy relationships in p21ras and related systems. Biochemistry. 35: 14232-43. PMID 8916908 DOI: 10.1021/Bi961119G  0.404
1996 Schweins T, Geyer M, Kalbitzer HR, Wittinghofer A, Warshel A. Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras. Biochemistry. 35: 14225-31. PMID 8916907 DOI: 10.1021/Bi961118O  0.365
1996 Muegge I, Schweins T, Langen R, Warshel A. Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. Structure (London, England : 1993). 4: 475-89. PMID 8740369 DOI: 10.1016/S0969-2126(96)00052-4  0.32
1996 Alden RG, Parson WW, Chu ZT, Warshel A. Orientation of the OH dipole of tyrosine (M)210 and its effect on electrostatic energies in photosynthetic bacterial reaction centers Journal of Physical Chemistry. 100: 16761-16770. DOI: 10.1021/Jp961271S  0.387
1996 Wesolowski T, Muller RP, Warshel A. Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution The Journal of Physical Chemistry. 100: 15444-15449. DOI: 10.1021/Jp961068X  0.39
1996 Hwang J, Warshel A. How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis? Journal of the American Chemical Society. 118: 11745-11751. DOI: 10.1021/Ja962007F  0.367
1996 Madura JD, Nakajima Y, Hamilton RM, Wierzbicki A, Warshel A. Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase Structural Chemistry. 7: 131-138. DOI: 10.1007/Bf02278738  0.394
1995 Schweins T, Geyer M, Scheffzek K, Warshel A, Kalbitzer HR, Wittinghofer A. Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins. Nature Structural Biology. 2: 36-44. PMID 7719852 DOI: 10.1038/Nsb0195-36  0.397
1995 Alden RG, Parson WW, Chu ZT, Warshel A. Calculations of electrostatic energies in photosynthetic reaction centers Journal of the American Chemical Society. 117: 12284-12298. DOI: 10.1021/Ja00154A031  0.416
1995 Fothergill M, Goodman MF, Petruska J, Warshel A. Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I Journal of the American Chemical Society. 117: 11619-11627. DOI: 10.1021/Ja00152A001  0.373
1995 Muller RP, Warshel A. Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution The Journal of Physical Chemistry. 99: 17516-17524. DOI: 10.1021/J100049A009  0.373
1994 Schweins T, Langen R, Warshel A. Why have mutagenesis studies not located the general base in ras p21. Nature Structural Biology. 1: 476-84. PMID 7664067 DOI: 10.1038/Nsb0794-476  0.31
1994 Warshel A, Schweins T, Fothergill M. Linear Free Energy Relationships in Enzymes. Theoretical Analysis of the Reaction of Tyrosyl-tRNA Synthetase Journal of the American Chemical Society. 116: 8437-8442. DOI: 10.1021/Ja00098A001  0.39
1994 Wesolowski T, Warshel A. Ab Initio Free Energy Perturbation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach The Journal of Physical Chemistry. 98: 5183-5187. DOI: 10.1021/J100071A003  0.403
1994 Warshel A, Chu ZT, Parson WW. On the energetics of the primary electron-transfer process in bacterial reaction centers Journal of Photochemistry and Photobiology, a: Chemistry. 82: 123-128. DOI: 10.1016/1010-6030(94)02010-8  0.393
1994 Warshel A, Tao H, Fothergill M, Chu Z. Effective Methods for Estimation of Binding Energies in Computer-Aided Drug Design Israel Journal of Chemistry. 34: 253-256. DOI: 10.1002/Ijch.199400029  0.358
1993 Pearson JG, Oldfield E, Lee FS, Warshel A. Chemical shifts in proteins: a shielding trajectory analysis of the fluorine nuclear magnetic resonance spectrum of the Escherichia coli galactose binding protein using a multipole shielding polarizability-local reaction field-molecular dynamics approach Journal of the American Chemical Society. 115: 6851-6862. DOI: 10.1021/Ja00068A049  0.348
1993 Hwang JK, Warshel A. A quantized classical path approach for calculations of quantum mechanical rate constants The Journal of Physical Chemistry. 97: 10053-10058. DOI: 10.1021/J100141A026  0.381
1993 Wesolowski TA, Warshel A. Frozen density functional approach for ab initio calculations of solvated molecules The Journal of Physical Chemistry. 97: 8050-8053. DOI: 10.1021/J100132A040  0.351
1993 Åqvist J, Warshel A. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches Chemical Reviews. 93: 2523-2544. DOI: 10.1021/Cr00023A010  0.324
1993 Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs Journal of Computational Chemistry. 14: 161-185. DOI: 10.1002/Jcc.540140205  0.448
1992 Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Engineering. 5: 215-28. PMID 1409541 DOI: 10.1093/Protein/5.3.215  0.411
1992 Langen R, Schweins T, Warshel A. On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins. Biochemistry. 31: 8691-6. PMID 1390653 DOI: 10.1021/Bi00152A002  0.369
1992 Warshel A, Hwang JK, Aqvist J. Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase. Faraday Discussions. 225-38. PMID 1337846 DOI: 10.1039/Fd9929300225  0.454
1992 Langen R, Brayer GD, Berghuis AM, McLendon G, Sherman F, Warshel A. Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment. Journal of Molecular Biology. 224: 589-600. PMID 1314900 DOI: 10.1016/0022-2836(92)90546-V  0.367
1992 Aqvist J, Warshel A. Computer simulation of the initial proton transfer step in human carbonic anhydrase I. Journal of Molecular Biology. 224: 7-14. PMID 1312606 DOI: 10.1016/0022-2836(92)90572-2  0.417
1992 Vaidehi N, Wesolowski TA, Warshel A. Quantum‐mechanical calculations of solvation free energies. A combinedabinitiopseudopotential free‐energy perturbation approach The Journal of Chemical Physics. 97: 4264-4271. DOI: 10.1063/1.463928  0.392
1992 Lee FS, Warshel A. A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations The Journal of Chemical Physics. 97: 3100-3107. DOI: 10.1063/1.462997  0.336
1992 Warshel A. Computer simulations of enzymatic reactions Current Opinion in Structural Biology. 2: 230-236. DOI: 10.1016/0959-440X(92)90151-V  0.379
1992 Luzhkov V, Warshel A. Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies Journal of Computational Chemistry. 13: 199-213. DOI: 10.1002/Jcc.540130212  0.342
1991 Aqvist J, Luecke H, Quiocho FA, Warshel A. Dipoles localized at helix termini of proteins stabilize charges. Proceedings of the National Academy of Sciences of the United States of America. 88: 2026-30. PMID 2000410 DOI: 10.1073/Pnas.88.5.2026  0.331
1991 King G, Lee FS, Warshel A. Microscopic simulations of macroscopic dielectric constants of solvated proteins The Journal of Chemical Physics. 95: 4366-4377. DOI: 10.1063/1.461760  0.35
1991 Yadav A, Jackson RM, Holbrook JJ, Warshel A. Role of solvent reorganization energies in the catalytic activity of enzymes Journal of the American Chemical Society. 113: 4800-4805. DOI: 10.1021/Ja00013A013  0.382
1991 Luzhkov V, Warshel A. Microscopic calculations of solvent effects on absorption spectra of conjugated molecules Journal of the American Chemical Society. 113: 4491-4499. DOI: 10.1021/Ja00012A018  0.312
1991 Hwang JK, Chu ZT, Yadav A, Warshel A. Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions The Journal of Physical Chemistry. 95: 8445-8448. DOI: 10.1021/J100175A009  0.332
1990 Parson WW, Chu ZT, Warshel A. Electrostatic control of charge separation in bacterial photosynthesis Bba - Bioenergetics. 1017: 251-272. PMID 2196939 DOI: 10.1016/0005-2728(90)90192-7  0.345
1990 King G, Warshel A. Investigation of the free energy functions for electron transfer reactions The Journal of Chemical Physics. 93: 8682-8692. DOI: 10.1063/1.459255  0.391
1990 Warshel A, Chu ZT. Quantum corrections for rate constants of diabatic and adiabatic reactions in solutions The Journal of Chemical Physics. 93: 4003-4015. DOI: 10.1063/1.458785  0.393
1990 Aaqvist J, Warshel A. Free energy relationships in metalloenzyme-catalyzed reactions. Calculations of the effects of metal ion substitutions in staphylococcal nuclease Journal of the American Chemical Society. 112: 2860-2868. DOI: 10.1021/Ja00164A003  0.347
1989 Aqvist J, Warshel A. Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction. Biochemistry. 28: 4680-9. PMID 2765507 DOI: 10.1021/Bi00437A026  0.463
1989 Warshel A, Aqvist J, Creighton S. Enzymes work by solvation substitution rather than by desolvation. Proceedings of the National Academy of Sciences of the United States of America. 86: 5820-4. PMID 2762299 DOI: 10.1073/Pnas.86.15.5820  0.398
1989 Warshel A, Chu ZT, Parson WW. Dispersed polaron simulations of electron transfer in photosynthetic reaction centers Science. 246: 112-116. PMID 2675313 DOI: 10.1126/Science.2675313  0.339
1989 Warshel A, Naray-Szabo G, Sussman F, Hwang JK. How do serine proteases really work? Biochemistry. 28: 3629-37. PMID 2665806 DOI: 10.1021/Bi00435A001  0.436
1989 Cutler RL, Davies AM, Creighton S, Warshel A, Moore GR, Smith M, Mauk AG. Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium. Biochemistry. 28: 3188-97. PMID 2545252 DOI: 10.1021/Bi00434A012  0.322
1989 King G, Warshel A. A surface constrained all‐atom solvent model for effective simulations of polar solutions The Journal of Chemical Physics. 91: 3647-3661. DOI: 10.1063/1.456845  0.304
1989 Parson WW, Creighton S, Warshel A. Calculations of charge-transfer transition energies and spectroscopic properties of a molecular crystal: Methylbacteriopheophorbide a Journal of the American Chemical Society. 111: 4277-4284. DOI: 10.1021/Ja00194A019  0.374
1989 Chu ZT, Warshel A, Parson WW. Microscopic simulation of quantum dynamics and nuclear tunneling in bacterial reaction centers Photosynthesis Research. 22: 39-46. DOI: 10.1007/Bf00114765  0.321
1988 Hwang JK, Warshel A. Why ion pair reversal by protein engineering is unlikely to succeed. Nature. 334: 270-2. PMID 3165161 DOI: 10.1038/334270A0  0.369
1988 Warshel A, Sussman F, Hwang JK. Evaluation of catalytic free energies in genetically modified proteins. Journal of Molecular Biology. 201: 139-59. PMID 3047396 DOI: 10.1016/0022-2836(88)90445-7  0.479
1988 Hwang J, Creighton S, King G, Whitney D, Warshel A. Effects of solute–solvent coupling and solvent saturation on solvation dynamics of charge transfer reactions The Journal of Chemical Physics. 89: 859-865. DOI: 10.1063/1.455719  0.351
1988 Hwang JK, King G, Creighton S, Warshel A. Simulation of free energy relationships and dynamics of SN2 reactions in aqueous solution Journal of the American Chemical Society. 110: 5297-5311. DOI: 10.1021/Ja00224A011  0.316
1988 Warshel A, Creighton S, Parson WW. Electron-transfer pathways in the primary event of bacterial photosynthesis Journal of Physical Chemistry. 92: 2696-2701. DOI: 10.1021/J100320A057  0.333
1988 Creighton S, Hwang JK, Warshel A, Parson WW, Norris J. Simulating the dynamics of the primary charge separation process in bacterial photosynthesis Biochemistry. 27: 774-781. DOI: 10.1021/Bi00402A043  0.399
1987 Hwang JK, Warshel A. Semiquantitative calculations of catalytic free energies in genetically modified enzymes. Biochemistry. 26: 2669-73. PMID 3300766 DOI: 10.1021/Bi00384A003  0.435
1987 Parson WW, Warshel A. Spectroscopic properties of photosynthetic reaction centers. 2. Application of the theory to Rhodopseudomonas viridis Journal of the American Chemical Society. 109: 6152-6163. DOI: 10.1021/Ja00254A040  0.327
1987 Hwang JK, Warshel A. Microscopic examination of free-energy relationships for electron transfer in polar solvents Journal of the American Chemical Society. 109: 715-720. DOI: 10.1021/Ja00237A013  0.437
1986 Warshel A, Sussman F. Toward computer-aided site-directed mutagenesis of enzymes. Proceedings of the National Academy of Sciences of the United States of America. 83: 3806-10. PMID 3520555 DOI: 10.1073/Pnas.83.11.3806  0.396
1986 Churg AK, Warshel A. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry. 25: 1675-81. PMID 3011070 DOI: 10.1021/Bi00355A035  0.396
1986 Warshel A, Hwang J. Simulation of the dynamics of electron transfer reactions in polar solvents: Semiclassical trajectories and dispersed polaron approaches The Journal of Chemical Physics. 84: 4938-4957. DOI: 10.1063/1.449981  0.395
1986 Warshel A, Russell S. Theoretical correlation of structure and energetics in the catalytic reaction of trypsin Journal of the American Chemical Society. 108: 6569-6579. DOI: 10.1021/Ja00281A021  0.302
1986 Warshel A, Russell S, Sussman F. Computer Simulation of Enzymatic Reactions Israel Journal of Chemistry. 27: 217-224. DOI: 10.1002/Ijch.198600031  0.423
1985 Warshel A, Russell ST. Calculations of electrostatic interactions in biological systems and in solutions. Quarterly Reviews of Biophysics. 17: 283-422. PMID 6098916 DOI: 10.1017/S0033583500005333  0.383
1985 Russell ST, Warshel A. Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. Journal of Molecular Biology. 185: 389-404. PMID 2414450 DOI: 10.1016/0022-2836(85)90411-5  0.431
1985 Warshel A, Hwang J. Quantized semiclassical trajectory approach for evaluation of vibronic transitions in anharmonic molecules The Journal of Chemical Physics. 82: 1756-1771. DOI: 10.1063/1.448408  0.358
1985 Warshel A, King G. Polarization constraints in molecular dynamics simulation of aqueous solutions: The surface constraint all atom solvent (SCAAS) model Chemical Physics Letters. 121: 124-129. DOI: 10.1016/0009-2614(85)87168-2  0.314
1985 Hwang J, Warshel A. Semiclassical simulations of the spectra of anharmonic molecules; problems and alternatives Chemical Physics Letters. 115: 281-285. DOI: 10.1016/0009-2614(85)80028-2  0.38
1984 Warshel A, Russell ST, Churg AK. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. Proceedings of the National Academy of Sciences of the United States of America. 81: 4785-9. PMID 6589625 DOI: 10.1073/Pnas.81.15.4785  0.365
1984 Warshel A. Dynamics of enzymatic reactions. Proceedings of the National Academy of Sciences of the United States of America. 81: 444-8. PMID 6582500 DOI: 10.1073/Pnas.81.2.444  0.373
1983 Warshel A, Stern PS, Mukamel S. Semiclassical calculation of electronic spectra of supercooled anharmonic molecules The Journal of Chemical Physics. 78: 7498-7500. DOI: 10.1063/1.444708  0.32
1982 Warshel A, Barboy N. Energy storage and reaction pathways in the first step of the vision process Journal of the American Chemical Society. 104: 1469-1476. DOI: 10.1021/Ja00370A003  0.336
1982 Warshel A, Barboy N. Energy storage and reaction pathways in the first step of the vision process Cheminform. 13. DOI: 10.1002/Chin.198226099  0.336
1981 Warshel A. Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry. 20: 3167-77. PMID 7248277 DOI: 10.1021/Bi00514A028  0.421
1981 Warshel A, Weiss RM. Empirical valence bond calculations of enzyme catalysis. Annals of the New York Academy of Sciences. 367: 370-82. PMID 6942759 DOI: 10.1111/J.1749-6632.1981.Tb50579.X  0.403
1981 Levitt M, Warshel A. Additions and Corrections - Extreme Conformational Flexibility of the Furanose 2607 in DNA and RNA Journal of the American Chemical Society. 103: 1879-1879. DOI: 10.1021/Ja00397A600  0.408
1981 Warshel A. Energetics of Light-Induced Charge Separation Across Membranes Israel Journal of Chemistry. 21: 341-347. DOI: 10.1002/Ijch.198100062  0.332
1980 Warshel A. Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium. Photochemistry and Photobiology. 30: 285-90. PMID 504352 DOI: 10.1111/J.1751-1097.1979.Tb07148.X  0.374
1980 Warshel A, Ottolenighi M. Kinetic and spectroscopic effects of protein-chromophore electrostatic interactions in bacteriorhodopsin. Photochemistry and Photobiology. 30: 291-3. PMID 41274 DOI: 10.1111/J.1751-1097.1979.Tb07149.X  0.339
1980 Warshel A, Weiss RM. An empirical valence bond approach for comparing reactions in solutions and in enzymes Journal of the American Chemical Society. 102: 6218-6226. DOI: 10.1002/Chin.198052105  0.339
1979 Warshel A. Energetics of enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. 75: 5250-4. PMID 281676 DOI: 10.1073/Pnas.75.11.5250  0.386
1978 Warshel A. Charge stabilization mechanism in the visual and purple membrane pigments. Proceedings of the National Academy of Sciences of the United States of America. 75: 2558-62. PMID 275826 DOI: 10.1073/Pnas.75.6.2558  0.377
1978 Levitt M, Warshel A. Extreme conformational flexibility of the furanose ring in DNA and RNA Journal of the American Chemical Society. 100: 2607-2613. DOI: 10.1021/Ja00477A004  0.402
1978 Cohen MD, Haberkorn R, Huler E, Ludmer Z, Michel-Beyerle ME, Rabinovich D, Sharon R, Warshel A, Yakhot V. Pair-states in α-perylene crystal. A theoretical study Chemical Physics. 27: 211-216. DOI: 10.1016/0301-0104(78)88005-7  0.315
1978 Warshel A, Deakyne C. Coupling of charge stabilization, torsion and bond alternation in light-induced reactions of visual pigments Chemical Physics Letters. 55: 459-465. DOI: 10.1016/0009-2614(78)84014-7  0.336
1978 Warshel A. A microscopic model for calculations of chemical processes in aqueous solutions Chemical Physics Letters. 55: 454-458. DOI: 10.1016/0009-2614(78)84013-5  0.36
1977 Warshel A. Energy-structure correlation in metalloporphyrins and the control of oxygen binding by hemoglobin. Proceedings of the National Academy of Sciences of the United States of America. 74: 1789-93. PMID 266703 DOI: 10.1073/Pnas.74.5.1789  0.377
1976 Warshel A. Bicycle-pedal model for the first step in the vision process. Nature. 260: 679-83. PMID 1264239 DOI: 10.1038/260679A0  0.325
1976 Warshel A, Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. Journal of Molecular Biology. 103: 227-49. PMID 985660 DOI: 10.1016/0022-2836(76)90311-9  0.568
1976 Warshel A, Levitt M. Folding and stability of helical proteins: carp myogen. Journal of Molecular Biology. 106: 421-37. PMID 978728 DOI: 10.1016/0022-2836(76)90094-2  0.5
1975 Levitt M, Warshel A. Computer simulation of protein folding. Nature. 253: 694-8. PMID 1167625 DOI: 10.1038/253694A0  0.511
1975 Levitt M, Warshel A. Folding proteins along the dotted lines (reply) Nature. 254: 388-388. DOI: 10.1038/254388A0  0.423
1975 Honig B, Warshel A, Karplus M. Theoretical studies of the visual chromophore Accounts of Chemical Research. 8: 92-100. DOI: 10.1021/Ar50087A003  0.532
1975 Warshel A, Karplus M. Semiclassical trajectory approach to photoisomerization Chemical Physics Letters. 32: 11-17. DOI: 10.1016/0009-2614(75)85157-8  0.5
1974 Rowan R, Warshel A, Sykes BD, Karplus M. Conformation of retinal isomers. Biochemistry. 13: 970-81. PMID 4813375 DOI: 10.1021/Bi00702A022  0.397
1974 Warshel A, Karplus M. Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules. Journal of the American Chemical Society. 96: 5677-89. PMID 4412283 DOI: 10.1021/Ja00825A001  0.439
1974 Warshel A, Huler E, Rabinovich D, Shakked Z. Examination of intramolecular potential surfaces of flexible conjugated molecules by calculation of crystal structures. equilibrium geometries of chalc Journal of Molecular Structure. 23: 175-191. DOI: 10.1016/0022-2860(74)85032-5  0.303
1974 WARSHEL A, KARPLUS M. ChemInform Abstract: CALCULATION OF PI,PI(*) EXCITED STATE CONFORMATIONS AND VIBRONIC STRUCTURE OF RETINAL AND RELATED MOLECULES Chemischer Informationsdienst. 5. DOI: 10.1002/Chin.197445099  0.44
1973 Warshel A. Quantum Mechanical Consistent Force Field (QCFF/PI) Method: Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited States of Conjugated Molecules Israel Journal of Chemistry. 11: 709-717. DOI: 10.1002/Ijch.197300067  0.343
1972 Warshel A, Karplus M. Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization Journal of the American Chemical Society. 94: 5612-5625. DOI: 10.1021/Ja00771A014  0.352
1972 Warshel A, Karplus M. Vibrational structure of electronic transitions in conjugated molecules Chemical Physics Letters. 17: 7-14. DOI: 10.1016/0009-2614(72)80311-7  0.442
1970 Warshel A, Lifson S. Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes The Journal of Chemical Physics. 53: 582-594. DOI: 10.1063/1.1674031  0.595
1970 Warshel A, Bromberg A. Oxidation of 4a,4b‐Dihydrophenanthrenes. III. A Theoretical Study of the Large Kinetic Isotope Effect of Deuterium in the Initiation Step of the Thermal Reaction with Oxygen The Journal of Chemical Physics. 52: 1262-1269. DOI: 10.1063/1.1673124  0.384
1970 Bromberg A, Muszkat KA, Warshel A. Oxidation of 4a,4b‐Dihydrophenanthrene. IV. Kinetic Isotope Effect of Deuterium in the Propagation and the Initiation Steps The Journal of Chemical Physics. 52: 5952-5959. DOI: 10.1063/1.1672879  0.309
1970 Warshel A, Levitt M, Lifson S. Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings Journal of Molecular Spectroscopy. 33: 84-99. DOI: 10.1016/0022-2852(70)90054-8  0.641
1970 WARSHEL A, LIFSON S. ChemInform Abstract: ′CONSISTENT FORCE FIELD′-(CFF)-BERECHNUNGEN 2. MITT. KRISTALLSTRUKTUREN, SUBLIMATIONSENERGIEN, MOLEKUEL- UND GITTERSCHWINGUNGEN, MOLEKUELKONFORMATIONEN UND ENTHALPIEN VON ALKANEN (N- UND CYCLOALKANE) Chemischer Informationsdienst. Organische Chemie. 1: no-no. DOI: 10.1002/Chin.197043164  0.519
1969 Warshel A, Lifson S. An empirical function for second neighbor interactions and its effect on vibrational modes and other properties of cyclo- and n-Alkanes Chemical Physics Letters. 4: 255-256. DOI: 10.1016/0009-2614(69)80177-6  0.576
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