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Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture).
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- Angewandte Chemie International Edition, 2014, v. 53, n. 38, p. 10020, doi. 10.1002/anie.201403689
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- Article
CONVERSION OF LIGHT ENERGY TO ELECTROSTATIC ENERGY IN THE PROTON PUMP OF HALOBACTERIUM HALOBIUM.
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- Photochemistry & Photobiology, 1979, v. 30, n. 2, p. 285, doi. 10.1111/j.1751-1097.1979.tb07148.x
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- Article
The FF ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function.
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- Photosynthesis Research, 2017, v. 134, n. 1, p. 1, doi. 10.1007/s11120-017-0411-x
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- Article
Computer simulation of protein folding.
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- Nature, 1975, v. 253, n. 5494, p. 694, doi. 10.1038/253694a0
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- Article
Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering.
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- National Science Review, 2023, v. 10, n. 12, p. 1, doi. 10.1093/nsr/nwad331
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- Article
The Physics and Physical Chemistry of Molecular Machines.
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- ChemPhysChem, 2016, v. 17, n. 12, p. 1719, doi. 10.1002/cphc.201600184
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- Article
Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models.
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- ChemPhysChem, 2009, v. 10, n. 7, p. 1125, doi. 10.1002/cphc.200800753
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Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies.
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- ChemPhysChem, 2008, v. 9, n. 12, p. 1767, doi. 10.1002/cphc.200800356
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- Article
Multiskalenmodellierung biologischer Funktionen: Von Enzymen zu molekularen Maschinen (Nobel-Aufsatz).
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- Angewandte Chemie, 2014, v. 126, n. 38, p. 10182, doi. 10.1002/ange.201403689
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- Article
Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting.
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- Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2012, v. 131, n. 12, p. 1, doi. 10.1007/s00214-012-1288-6
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An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling.
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- Journal of Physical Organic Chemistry, 2010, v. 23, n. 7, p. 677, doi. 10.1002/poc.1620
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- Article
The empirical valence bond as an effective strategy for computer-aided enzyme design.
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- Biotechnology Journal, 2009, v. 4, n. 4, p. 495, doi. 10.1002/biot.200800299
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Refining the treatment of membrane proteins by coarse-grained models.
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- Proteins, 2016, v. 84, n. 1, p. 92, doi. 10.1002/prot.24958
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- Article
Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.
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- Proteins, 2015, v. 83, n. 2, p. 318, doi. 10.1002/prot.24717
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An effective Coarse-grained model for biological simulations: Recent refinements and validations.
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- Proteins, 2014, v. 82, n. 7, p. 1168, doi. 10.1002/prot.24482
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Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B.
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- Proteins, 2014, v. 82, n. 7, p. 1387, doi. 10.1002/prot.24506
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- Article
Capturing the energetics of water insertion in biological systems: The water flooding approach.
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- Proteins, 2013, v. 81, n. 1, p. 93, doi. 10.1002/prot.24165
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Validating the vitality strategy for fighting drug resistance.
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- Proteins, 2012, v. 80, n. 4, p. 1110, doi. 10.1002/prot.24012
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Simulating electrostatic energies in proteins: Perspectives and some recent studies of p K<sub>a</sub>s, redox, and other crucial functional properties.
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- Proteins, 2011, v. 79, n. 12, p. 3469, doi. 10.1002/prot.23125
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Prechemistry versus preorganization in DNA replication fidelity.
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- Proteins, 2011, v. 79, n. 10, p. 2900, doi. 10.1002/prot.23128
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Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models.
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- Proteins, 2010, v. 78, n. 5, p. 1212, doi. 10.1002/prot.22640
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Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions.
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- Proteins, 2010, v. 78, n. 7, p. 1705, doi. 10.1002/prot.22687
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A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.
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- Proteins, 2010, v. 78, n. 7, p. 1724, doi. 10.1002/prot.22689
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At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
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- Proteins, 2010, v. 78, n. 6, p. 1339, doi. 10.1002/prot.22654
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A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.
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- Proteins, 2010, v. 78, n. 3, p. 671, doi. 10.1002/prot.22596
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On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes.
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- Proteins, 2009, v. 77, n. 3, p. 536, doi. 10.1002/prot.22466
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Effective approach for calculations of absolute stability of proteins using focused dielectric constants.
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- Proteins, 2009, v. 77, n. 3, p. 670, doi. 10.1002/prot.22481
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- Article
Exploring the role of large conformational changes in the fidelity of DNA polymerase β.
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- Proteins, 2008, v. 70, n. 1, p. 231, doi. 10.1002/prot.21668
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The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations.
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- Proteins, 2006, v. 64, n. 4, p. 829, doi. 10.1002/prot.21012
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The low barrier hydrogen bond (LBHB) proposal revisited: The case of the Asp ··· His pair in serine proteases.
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- Proteins, 2004, v. 55, n. 3, p. 711, doi. 10.1002/prot.20096
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- Article
Why does the Ras switch break by oncogenic mutations?
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- Proteins, 2004, v. 55, n. 1, p. 1, doi. 10.1002/prot.20004
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Exploring the origin of the ion selectivity of the KcsA potassium channel.
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- Proteins, 2003, v. 52, n. 3, p. 412, doi. 10.1002/prot.10455
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- Article
What are the dielectric 'constants' of proteins and how to validate electrostatic models?
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- Proteins, 2001, v. 44, n. 4, p. 400, doi. 10.1002/prot.1106
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Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
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- Proteins, 2000, v. 39, n. 4, p. 393, doi. 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.0.CO;2-H
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Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center.
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- Proteins, 1999, v. 36, n. 4, p. 484, doi. 10.1002/(SICI)1097-0134(19990901)36:4<484::AID-PROT13>3.0.CO;2-R
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- Article
Electrostatic contributions to protein-protein binding affinities: Application to Rap/Raf interaction.
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- Proteins, 1998, v. 30, n. 4, p. 407, doi. 10.1002/(SICI)1097-0134(19980301)30:4<407::AID-PROT8>3.0.CO;2-F
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Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes.
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- Journal of Biological Inorganic Chemistry (JBIC), 2004, v. 9, n. 1, p. 96, doi. 10.1007/s00775-003-0503-2
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Why ion pair reversal by protein engineering is unlikely to succeed.
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- Nature, 1988, v. 334, n. 6179, p. 270, doi. 10.1038/334270a0
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What about protein polarity?
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- Nature, 1987, v. 330, n. 6143, p. 15, doi. 10.1038/330015a0
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- Article
Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A.
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- ChemBioChem, 2012, v. 13, n. 2, p. 215, doi. 10.1002/cbic.201100600
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- Article
The empirical valence bond model: theory and applications.
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- WIREs: Computational Molecular Science, 2011, v. 1, n. 1, p. 30, doi. 10.1002/wcms.10
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- Article
Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase.
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- Quarterly Reviews of Biophysics, 2015, v. 48, n. 4, p. 395, doi. 10.1017/S0033583515000050
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Calculations of electrostatic interactions in biological systems and in solutions.
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- Quarterly Reviews of Biophysics, 1984, v. 17, n. 3, p. 283, doi. 10.1017/S0033583500005333
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Computer simulation studies of the fidelity of DNA polymerases.
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- Biopolymers, 2003, v. 68, n. 3, p. 286, doi. 10.1002/bip.10244
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- Article
Constraining the electron densities in DFT method as an effective way for ab initio studies of metal-catalyzed reactions.
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- Journal of Computational Chemistry, 2000, v. 21, n. 16, p. 1554, doi. 10.1002/1096-987X(200012)21:16<1554::AID-JCC12>3.0.CO;2-I
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- Article
Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions.
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- Journal of Computational Chemistry, 2000, v. 21, n. 8, p. 607, doi. 10.1002/(SICI)1096-987X(200006)21:8<607::AID-JCC3>3.0.CO;2-R
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Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs.
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- Journal of Computational Chemistry, 1993, v. 14, n. 2, p. 161, doi. 10.1002/jcc.540140205
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- Article
Electrostatic contributions to protein stability and folding energy
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- FEBS Letters, 2007, v. 581, n. 10, p. 2065, doi. 10.1016/j.febslet.2007.04.025
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- Article
DNA polymerase β catalytic efficiency mirrors the Asn279–dCTP H-bonding strength
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- FEBS Letters, 2007, v. 581, n. 4, p. 775, doi. 10.1016/j.febslet.2007.01.042
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- Article
Simulating redox coupled proton transfer in cytochrome c oxidase: Looking for the proton bottleneck
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- FEBS Letters, 2005, v. 579, n. 10, p. 2026, doi. 10.1016/j.febslet.2005.02.051
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- Article