| Year |
Citation |
Score |
| 2023 |
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, ... Levy RM, et al. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Science Advances. 9: eadg5953. PMID 37478179 DOI: 10.1126/sciadv.adg5953 |
0.602 |
|
| 2022 |
Choudhuri I, Biswas A, Haldane A, Levy RM. Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins. The Journal of Physical Chemistry. B. 126: 10622-10636. PMID 36493468 DOI: 10.1021/acs.jpcb.2c06123 |
0.614 |
|
| 2021 |
Haldane A, Levy RM. Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis Computer Physics Communications. 260: 107312. DOI: 10.1016/J.Cpc.2020.107312 |
0.334 |
|
| 2020 |
Tse C, Wickstrom L, Kvaratskhelia M, Gallicchio E, Levy R, Deng N. Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. Biophysical Journal. PMID 32877664 DOI: 10.1016/J.Bpj.2020.08.005 |
0.665 |
|
| 2020 |
Zhang BW, Matubayasi N, Levy RM. Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. The Journal of Physical Chemistry. B. PMID 32469519 DOI: 10.1021/Acs.Jpcb.0C02721 |
0.316 |
|
| 2020 |
Levy RM. Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling. Proceedings of the National Academy of Sciences of the United States of America. PMID 31924744 DOI: 10.1073/Pnas.1921727117 |
0.368 |
|
| 2019 |
Narayan B, Fathizadeh A, Templeton C, He P, Arasteh S, Elber R, Buchete NV, Levy RM. The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochimica Et Biophysica Acta. General Subjects. 129508. PMID 31884066 DOI: 10.1016/J.Bbagen.2019.129508 |
0.507 |
|
| 2019 |
Cui D, Zhang BW, Tan Z, Levy RM. Ligand Binding Thermodynamic Cycles: Hysteresis, LWHAM, and the Overlapping States Matrix. Journal of Chemical Theory and Computation. PMID 31743019 DOI: 10.1021/Acs.Jctc.9B00740 |
0.37 |
|
| 2019 |
Sakae Y, Zhang BW, Levy RM, Deng N. Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. Journal of Computational Chemistry. PMID 31621932 DOI: 10.1002/Jcc.26078 |
0.395 |
|
| 2019 |
Ishii Y, Yamamoto N, Matubayasi N, Zhang BW, Cui D, Levy RM. Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. Journal of Chemical Theory and Computation. PMID 30990682 DOI: 10.1021/Acs.Jctc.8B01309 |
0.348 |
|
| 2019 |
Zhang BW, Arasteh S, Levy RM. The UWHAM and SWHAM Software Package. Scientific Reports. 9: 2803. PMID 30808938 DOI: 10.1038/S41598-019-39420-X |
0.329 |
|
| 2019 |
Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. Journal of Chemical Information and Modeling. PMID 30758197 DOI: 10.1021/Acs.Jcim.8B00817 |
0.675 |
|
| 2018 |
He P, Zhang BW, Arasteh S, Wang L, Abel R, Levy RM. Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters. PMID 30024165 DOI: 10.1021/Acs.Jpclett.8B01851 |
0.337 |
|
| 2018 |
Xia J, Flynn WF, Levy RM. On Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of Chemical Information and Modeling. PMID 29927237 DOI: 10.1021/Acs.Jcim.8B00194 |
0.455 |
|
| 2018 |
Deng N, Cui D, Zhang BW, Xia J, Cruz J, Levy R. Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Physical Chemistry Chemical Physics : Pccp. PMID 29896599 DOI: 10.1039/C8Cp01524D |
0.389 |
|
| 2018 |
Zhang BW, Cui D, Matubayasi N, Levy RM. The Excess Chemical Potential of Water at the Interface with a Protein from Endpoint Simulations. The Journal of Physical Chemistry. B. PMID 29634902 DOI: 10.1021/Acs.Jpcb.8B02666 |
0.378 |
|
| 2017 |
Cui D, Zhang BW, Matubayasi N, Levy RM. The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated PMF. Journal of Chemical Theory and Computation. PMID 29262255 DOI: 10.1021/Acs.Jctc.7B01076 |
0.373 |
|
| 2017 |
Zhang BW, Deng N, Tan Z, Levy RM. Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which are Far from Equilibrium. Journal of Chemical Theory and Computation. PMID 28902500 DOI: 10.1021/Acs.Jctc.7B00651 |
0.407 |
|
| 2017 |
Levy RM, Cui D, Zhang BW, Matubayasi N. The Relationship Between Solvation Thermodynamics from IST and DFT Perspectives. The Journal of Physical Chemistry. B. PMID 28186751 DOI: 10.1021/Acs.Jpcb.6B12889 |
0.346 |
|
| 2016 |
Harris RC, Deng N, Levy RM, Ishizuka R, Matubayasi N. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. Journal of Computational Chemistry. PMID 28008630 DOI: 10.1002/Jcc.24668 |
0.374 |
|
| 2016 |
Levy RM, Haldane A, Flynn WF. Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Current Opinion in Structural Biology. 43: 55-62. PMID 27870991 DOI: 10.1016/J.Sbi.2016.11.004 |
0.353 |
|
| 2016 |
Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design. PMID 27815770 DOI: 10.1007/s10822-016-9987-z |
0.779 |
|
| 2016 |
Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design. PMID 27696239 DOI: 10.1007/S10822-016-9956-6 |
0.8 |
|
| 2016 |
Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. Journal of Computer-Aided Molecular Design. PMID 27562018 DOI: 10.1007/S10822-016-9952-X |
0.653 |
|
| 2016 |
Deng N, Hoyte A, Mansour YE, Mohamed MS, Fuchs JR, Engelman AN, Kvaratskhelia M, Levy R. Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies. Protein Science : a Publication of the Protein Society. 25: 1911-1917. PMID 27503276 DOI: 10.1002/Pro.2997 |
0.367 |
|
| 2016 |
Haldane A, Flynn WF, He P, Vijayan RS, Levy RM. Structural Propensities of Kinase Family Proteins from a Potts Model of Residue Co-Variation. Protein Science : a Publication of the Protein Society. PMID 27241634 DOI: 10.1002/Pro.2954 |
0.378 |
|
| 2016 |
Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM. Simulating Replica Exchange: Markov State Models, Proposal Schemes and the Infinite Swapping Limit. The Journal of Physical Chemistry. B. PMID 27079355 DOI: 10.1021/Acs.Jpcb.6B02015 |
0.654 |
|
| 2016 |
Mentes A, Deng NJ, Vijayan RS, Xia J, Gallicchio E, Levy RM. Binding Energy Distribution Analysis Method (BEDAM): Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation. Journal of Chemical Theory and Computation. PMID 27070865 DOI: 10.1021/Acs.Jctc.6B00134 |
0.679 |
|
| 2016 |
Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis. Journal of Computational Chemistry. 37. PMID 26860348 DOI: 10.1002/jcc.24336 |
0.578 |
|
| 2016 |
Tan Z, Xia J, Zhang BW, Levy RM. Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. The Journal of Chemical Physics. 144: 034107. PMID 26801020 DOI: 10.1063/1.4939768 |
0.398 |
|
| 2016 |
Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition : Jmr. 29: 10-21. PMID 26256816 DOI: 10.1002/Jmr.2489 |
0.658 |
|
| 2015 |
Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing. Computer Physics Communications. 196: 236-246. PMID 27103749 DOI: 10.1016/J.Cpc.2015.06.010 |
0.628 |
|
| 2015 |
Zhang BW, Xia J, Tan Z, Levy RM. A Stochastic Solution to the Unbinned WHAM Equations. The Journal of Physical Chemistry Letters. 6: 3834-3840. PMID 26722879 DOI: 10.1021/Acs.Jpclett.5B01771 |
0.385 |
|
| 2015 |
Dai W, Sengupta AM, Levy RM. First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins. Physical Review Letters. 115: 048101. PMID 26252709 DOI: 10.1103/Physrevlett.115.048101 |
0.337 |
|
| 2015 |
Deng N, Zhang BW, Levy RM. Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies. Journal of Chemical Theory and Computation. 11: 2868-2878. PMID 26236174 DOI: 10.1021/Acs.Jctc.5B00264 |
0.417 |
|
| 2015 |
Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of Computational Chemistry. PMID 26149645 DOI: 10.1002/Jcc.23996 |
0.65 |
|
| 2015 |
Gallicchio E, Chen H, Chen H, Fitzgerald M, Gao Y, He P, Kalyanikar M, Kao C, Lu B, Niu Y, Pethe M, Zhu J, Levy RM. BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. Journal of Computer-Aided Molecular Design. 29: 315-25. PMID 25726024 DOI: 10.1007/S10822-014-9795-2 |
0.645 |
|
| 2015 |
Vijayan RS, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. Journal of Medicinal Chemistry. 58: 466-79. PMID 25478866 DOI: 10.1021/Jm501603H |
0.566 |
|
| 2015 |
Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. The Journal of Physical Chemistry. B. 119: 976-88. PMID 25189630 DOI: 10.1021/Jp506376Z |
0.659 |
|
| 2015 |
Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A, Levy RM. Asynchronous replica exchange software for grid and heterogeneous computing Computer Physics Communications. DOI: 10.1016/j.cpc.2015.06.010 |
0.531 |
|
| 2015 |
Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data Journal of Molecular Recognition. DOI: 10.1002/jmr.2489 |
0.585 |
|
| 2014 |
Xia J, Levy RM. Molecular dynamics of the proline switch and its role in Crk signaling. The Journal of Physical Chemistry. B. 118: 4535-45. PMID 24702481 DOI: 10.1021/Jp5013297 |
0.325 |
|
| 2014 |
Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 475-90. PMID 24504704 DOI: 10.1007/S10822-014-9711-9 |
0.672 |
|
| 2013 |
Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. Journal of Chemical Theory and Computation. 9: 3136-3150. PMID 25147485 DOI: 10.1021/Ct400003R |
0.673 |
|
| 2013 |
Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF. Correction: Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses. Plos One. 8. PMID 24116242 DOI: 10.1371/Annotation/57Fc0148-19Fe-4B8B-B2F4-Bb5F60Baa971 |
0.563 |
|
| 2013 |
Yi G, Lapelosa M, Bradley R, Mariano TM, Dietz DE, Hughes S, Wrin T, Petropoulos C, Gallicchio E, Levy RM, Arnold E, Arnold GF. Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses. Plos One. 8: e72205. PMID 24039745 DOI: 10.1371/Journal.Pone.0072205 |
0.563 |
|
| 2013 |
Deng NJ, Dai W, Levy RM. How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. The Journal of Physical Chemistry. B. 117: 12787-99. PMID 23705683 DOI: 10.1021/Jp401962K |
0.365 |
|
| 2013 |
Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. The Journal of Physical Chemistry. B. 117: 6625-34. PMID 23638941 DOI: 10.1021/Jp400797Y |
0.42 |
|
| 2013 |
Radak BK, Romanus M, Gallicchio E, Lee TS, Weidner O, Deng NJ, He P, Dai W, York DM, Levy RM, Jha S. A framework for flexible and scalable replica-exchange on production distributed CI Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484830 |
0.641 |
|
| 2012 |
Narayanan C, Weinstock DS, Wu KP, Baum J, Levy RM. Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. Journal of Chemical Theory and Computation. 8: 3929-3942. PMID 23162382 DOI: 10.1021/Ct300241T |
0.748 |
|
| 2012 |
Tan Z, Gallicchio E, Lapelosa M, Levy RM. Theory of binless multi-state free energy estimation with applications to protein-ligand binding. The Journal of Chemical Physics. 136: 144102. PMID 22502496 DOI: 10.1063/1.3701175 |
0.661 |
|
| 2012 |
Lapelosa M, Gallicchio E, Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation. 8: 47-60. PMID 22368530 DOI: 10.1021/Ct200684B |
0.68 |
|
| 2012 |
Gallicchio E, Levy RM. Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). Journal of Computer-Aided Molecular Design. 26: 505-16. PMID 22354755 DOI: 10.1007/S10822-012-9552-3 |
0.675 |
|
| 2012 |
Wickstrom L, Gallicchio E, Levy RM. The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins. 80: 111-25. PMID 22038697 DOI: 10.1002/Prot.23168 |
0.624 |
|
| 2012 |
Bell JA, Cao Y, Gunn JR, Day T, Gallicchio E, Zhou Z, Levy R, Farid R. PrimeX and the Schrödinger computational chemistry suite of programs International Tables For Crystallography. DOI: 10.1107/97809553602060000864 |
0.612 |
|
| 2011 |
Gallicchio E, Levy RM. Recent theoretical and computational advances for modeling protein-ligand binding affinities. Advances in Protein Chemistry and Structural Biology. 85: 27-80. PMID 21920321 DOI: 10.1016/B978-0-12-386485-7.00002-8 |
0.655 |
|
| 2011 |
Deng NJ, Zheng W, Gallicchio E, Levy RM. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. Journal of the American Chemical Society. 133: 9387-94. PMID 21561098 DOI: 10.1021/Ja2008032 |
0.413 |
|
| 2011 |
Gallicchio E, Levy RM. Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology. 21: 161-6. PMID 21339062 DOI: 10.1016/J.Sbi.2011.01.010 |
0.662 |
|
| 2011 |
Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM. Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. The Journal of Physical Chemistry. B. 115: 1512-23. PMID 21254767 DOI: 10.1021/Jp1089596 |
0.653 |
|
| 2010 |
Gallicchio E, Lapelosa M, Levy RM. The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. Journal of Chemical Theory and Computation. 6: 2961-2977. PMID 21116484 DOI: 10.1021/Ct1002913 |
0.656 |
|
| 2010 |
Lapelosa M, Arnold GF, Gallicchio E, Arnold E, Levy RM. Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. Journal of Molecular Biology. 397: 752-66. PMID 20138057 DOI: 10.1016/J.Jmb.2010.01.064 |
0.623 |
|
| 2010 |
Okumura H, Gallicchio E, Levy RM. Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. Journal of Computational Chemistry. 31: 1357-67. PMID 19882731 DOI: 10.1002/Jcc.21419 |
0.66 |
|
| 2010 |
Sheridan RP, Levy RM, Englander SW. Normal mode paths for hydrogen exchange in the peptide ferrichrome. Proceedings of the National Academy of Sciences of the United States of America. 80: 5569-72. PMID 16593367 DOI: 10.1073/Pnas.80.18.5569 |
0.31 |
|
| 2010 |
Levy RM, Perahia D, Karplus M. Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proceedings of the National Academy of Sciences of the United States of America. 79: 1346-50. PMID 16593164 DOI: 10.1073/Pnas.79.4.1346 |
0.629 |
|
| 2010 |
Lapelosa M, Arnold GF, Gallicchio E, Arnold E, Levy RM. Erratum to “Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for Enhanced Presentation of HIV-1 gp41 Epitopes” [J. Mol. Biol. 397 (2010) 752–766] Journal of Molecular Biology. 398: 623-624. DOI: 10.1016/J.Jmb.2010.03.044 |
0.551 |
|
| 2010 |
Zheng W, Gallicchio E, Andrec M, Levy RM. Exploring the Kinetics and Folding Pathways of Trp-cage using a Kinetic Network Model Biophysical Journal. 98: 634a. DOI: 10.1016/J.Bpj.2009.12.3472 |
0.628 |
|
| 2009 |
Gallicchio E, Paris K, Levy RM. The AGBNP2 Implicit Solvation Model. Journal of Chemical Theory and Computation. 5: 2544-2564. PMID 20419084 DOI: 10.1021/Ct900234U |
0.654 |
|
| 2009 |
Paris KA, Haq O, Felts AK, Das K, Arnold E, Levy RM. Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures. Journal of Medicinal Chemistry. 52: 6413-20. PMID 19827836 DOI: 10.1021/Jm900854H |
0.327 |
|
| 2009 |
Frenkel YV, Gallicchio E, Das K, Levy RM, Arnold E. Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability. Journal of Medicinal Chemistry. 52: 5896-905. PMID 19739675 DOI: 10.1021/Jm900282Z |
0.606 |
|
| 2009 |
Zheng W, Andrec M, Gallicchio E, Levy RM. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. The Journal of Physical Chemistry. B. 113: 11702-9. PMID 19655770 DOI: 10.1021/Jp900445T |
0.625 |
|
| 2009 |
Wu KP, Weinstock DS, Narayanan C, Levy RM, Baum J. Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. Journal of Molecular Biology. 391: 784-96. PMID 19576220 DOI: 10.1016/J.Jmb.2009.06.063 |
0.728 |
|
| 2009 |
Lapelosa M, Gallicchio E, Arnold GF, Arnold E, Levy RM. In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. Journal of Molecular Biology. 385: 675-91. PMID 19026659 DOI: 10.1016/J.Jmb.2008.10.089 |
0.627 |
|
| 2008 |
Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Journal of Chemical Theory and Computation. 4: 855-868. PMID 18787648 DOI: 10.1021/Ct800051K |
0.666 |
|
| 2008 |
Weinstock DS, Narayanan C, Baum J, Levy RM. Correlation between 13Calpha chemical shifts and helix content of peptide ensembles. Protein Science : a Publication of the Protein Society. 17: 950-4. PMID 18436960 DOI: 10.1110/Ps.073365408 |
0.745 |
|
| 2008 |
Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallographica. Section D, Biological Crystallography. 64: 383-96. PMID 18391405 DOI: 10.1107/S090744490800070X |
0.639 |
|
| 2008 |
Zheng W, Andrec M, Gallicchio E, Levy RM. Simple continuous and discrete models for simulating replica exchange simulations of protein folding. The Journal of Physical Chemistry. B. 112: 6083-93. PMID 18251533 DOI: 10.1021/Jp076377+ |
0.657 |
|
| 2008 |
Gallicchio E, Levy RM, Parashar M. Asynchronous replica exchange for molecular simulations. Journal of Computational Chemistry. 29: 788-94. PMID 17876761 DOI: 10.1002/Jcc.20839 |
0.613 |
|
| 2007 |
Su Y, Gallicchio E, Das K, Arnold E, Levy RM. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase. Journal of Chemical Theory and Computation. 3: 256-77. PMID 26627170 DOI: 10.1021/Ct600258E |
0.646 |
|
| 2007 |
Zheng W, Andrec M, Gallicchio E, Levy RM. Simulating replica exchange simulations of protein folding with a kinetic network model. Proceedings of the National Academy of Sciences of the United States of America. 104: 15340-5. PMID 17878309 DOI: 10.1073/Pnas.0704418104 |
0.659 |
|
| 2007 |
Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins. 69: 449-65. PMID 17623851 DOI: 10.1002/Prot.21507 |
0.323 |
|
| 2007 |
Weinstock DS, Narayanan C, Felts AK, Andrec M, Levy RM, Wu KP, Baum J. Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. Journal of the American Chemical Society. 129: 4858-9. PMID 17402734 DOI: 10.1021/Ja0677517 |
0.753 |
|
| 2007 |
Ravindranathan KP, Gallicchio E, McDermott AE, Levy RM. Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: Insights from NMR order parameters Journal of the American Chemical Society. 129: 474-475. PMID 17226994 DOI: 10.1021/Ja0672371 |
0.634 |
|
| 2006 |
Himmel DM, Sarafianos SG, Dharmasena S, Hossain MM, McCoy-Simandle K, Ilina T, Clark AD, Knight JL, Julias JG, Clark PK, Krogh-Jespersen K, Levy RM, Hughes SH, Parniak MA, Arnold E. HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. Acs Chemical Biology. 1: 702-12. PMID 17184135 DOI: 10.1021/Cb600303Y |
0.304 |
|
| 2006 |
Ravindranathan KP, Gallicchio E, Friesner RA, McDermott AE, Levy RM. Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. Journal of the American Chemical Society. 128: 5786-91. PMID 16637647 DOI: 10.1021/Ja058465I |
0.646 |
|
| 2006 |
Zhang L, Parashar M, Gallicchio E, Levy RM. Salsa: Scalable asynchronous replica exchange for parallel molecular dynamics applications Proceedings of the International Conference On Parallel Processing. 127-134. DOI: 10.1109/ICPP.2006.63 |
0.569 |
|
| 2005 |
Gallicchio E, Andrec M, Felts AK, Levy RM. Temperature weighted histogram analysis method, replica exchange, and transition paths. The Journal of Physical Chemistry. B. 109: 6722-31. PMID 16851756 DOI: 10.1021/Jp045294F |
0.642 |
|
| 2005 |
Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, ... ... Levy RM, et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry. 26: 1752-80. PMID 16211539 DOI: 10.1002/Jcc.20292 |
0.696 |
|
| 2005 |
Ravindranathan KP, Gallicchio E, Levy RM. Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. Journal of Molecular Biology. 353: 196-210. PMID 16157349 DOI: 10.1016/J.Jmb.2005.08.009 |
0.671 |
|
| 2005 |
Andrec M, Felts AK, Gallicchio E, Levy RM. Protein folding pathways from replica exchange simulations and a kinetic network model. Proceedings of the National Academy of Sciences of the United States of America. 102: 6801-6. PMID 15800044 DOI: 10.1073/Pnas.0408970102 |
0.649 |
|
| 2005 |
Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophysical Journal. 88: 925-38. PMID 15542547 DOI: 10.1529/Biophysj.104.050187 |
0.338 |
|
| 2004 |
Felts AK, Harano Y, Gallicchio E, Levy RM. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins. 56: 310-21. PMID 15211514 DOI: 10.1002/Prot.20104 |
0.636 |
|
| 2004 |
Gallicchio E, Levy RM. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. Journal of Computational Chemistry. 25: 479-99. PMID 14735568 DOI: 10.1002/Jcc.10400 |
0.68 |
|
| 2004 |
Chekmarev DS, Ishida T, Levy RM. Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models The Journal of Physical Chemistry B. 108: 19487-19495. DOI: 10.1021/Jp048540W |
0.406 |
|
| 2003 |
Andrec M, Levy RM, Talaga DS. Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. The Journal of Physical Chemistry. A. 107: 7454-7464. PMID 19626138 DOI: 10.1021/Jp035514+ |
0.303 |
|
| 2003 |
Levy RM, Zhang LY, Gallicchio E, Felts AK. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. Journal of the American Chemical Society. 125: 9523-30. PMID 12889983 DOI: 10.1021/Ja029833A |
0.677 |
|
| 2003 |
Du P, Andrec M, Levy RM. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Engineering. 16: 407-14. PMID 12874373 DOI: 10.1093/Protein/Gzg052 |
0.305 |
|
| 2002 |
Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054 |
0.378 |
|
| 2002 |
Andrec M, Levy RM. Protein sequential resonance assignments by combinatorial enumeration using 13C alpha chemical shifts and their (i, i-1) sequential connectivities. Journal of Biomolecular Nmr. 23: 263-70. PMID 12398347 DOI: 10.1023/A:1020236105735 |
0.323 |
|
| 2002 |
Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins. 48: 404-22. PMID 12112706 DOI: 10.1002/Prot.10171 |
0.655 |
|
| 2002 |
Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. Journal of Computational Chemistry. 23: 517-29. PMID 11948578 DOI: 10.1002/Jcc.10045 |
0.661 |
|
| 2002 |
Andrec M, Du P, Levy RM. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. Journal of Biomolecular Nmr. 21: 335-47. PMID 11824753 DOI: 10.1023/A:1013334513610 |
0.349 |
|
| 2002 |
Kubo M, Levy RM, Rossky PJ, Matubayasi N, Nakahara M. Chloride ion hydration and diffusion in supercritical water using a polarizable water model Journal of Physical Chemistry B. 106: 3979-3986. DOI: 10.1021/Jp013743V |
0.507 |
|
| 2001 |
Andrec M, Du P, Levy RM. Protein structural motif recognition via NMR residual dipolar couplings. Journal of the American Chemical Society. 123: 1222-9. PMID 11456677 DOI: 10.1021/Ja003979X |
0.35 |
|
| 2001 |
Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z |
0.367 |
|
| 2001 |
Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations Journal of Computational Chemistry. 22: 591-607. DOI: 10.1002/Jcc.1031 |
0.676 |
|
| 2000 |
Andrec M, Inman KG, Weber DJ, Levy RM, Montelione GT. A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 146: 66-80. PMID 10968959 DOI: 10.1006/Jmre.2000.2113 |
0.303 |
|
| 2000 |
Andrec M, Montelione GT, Levy RM. Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 139: 408-21. PMID 10423379 DOI: 10.1006/Jmre.1999.1839 |
0.309 |
|
| 2000 |
Lockwood DM, Rossky PJ, Levy RM. Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water Journal of Physical Chemistry B. 104: 4210-4217. DOI: 10.1021/Jp994197X |
0.506 |
|
| 2000 |
Gallicchio E, Kubo MM, Levy RM. Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation The Journal of Physical Chemistry B. 104: 6271-6285. DOI: 10.1021/Jp0006274 |
0.646 |
|
| 1999 |
Levy RM, Gallicchio E. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annual Review of Physical Chemistry. 49: 531-67. PMID 9933909 DOI: 10.1146/Annurev.Physchem.49.1.531 |
0.665 |
|
| 1999 |
Jin D, Andrec M, Montelione GT, Levy RM. Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. Journal of Biomolecular Nmr. 12: 471-92. PMID 9862126 DOI: 10.1023/A:1008313319334 |
0.327 |
|
| 1999 |
Murphy LR, Li N, Baum J, Levy RM. Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study. Journal of Biomolecular Structure & Dynamics. 16: 355-65. PMID 9833674 DOI: 10.1080/07391102.1998.10508253 |
0.339 |
|
| 1998 |
Murphy LR, Matubayasi N, Payne VA, Levy RM. Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models. Folding & Design. 3: 105-18. PMID 9565755 DOI: 10.1016/S1359-0278(98)00016-9 |
0.332 |
|
| 1998 |
Matubayasi N, Gallicchio E, Levy RM. On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models The Journal of Chemical Physics. 109: 4864-4872. DOI: 10.1063/1.477097 |
0.607 |
|
| 1998 |
Gallicchio E, Kubo MM, Levy RM. Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited Journal of the American Chemical Society. 120: 4526-4527. DOI: 10.1021/Ja974061H |
0.606 |
|
| 1997 |
Figueirido F, Levy RM, Zhou R, Berne BJ. Erratum: “Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators” [J. Chem. Phys. 106, 9835 (1997)] The Journal of Chemical Physics. 107: 7002-7002. DOI: 10.1063/1.475334 |
0.502 |
|
| 1997 |
Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators The Journal of Chemical Physics. 106: 9835-9849. DOI: 10.1063/1.474115 |
0.429 |
|
| 1997 |
Figueirido F, Levy RM, Zhou R, Berne BJ. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators Journal of Chemical Physics. 106: 9835-9849. DOI: 10.1063/1.474115 |
0.524 |
|
| 1997 |
Kubo MM, Gallicchio E, Levy RM. Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides The Journal of Physical Chemistry B. 101: 10527-10534. DOI: 10.1021/Jp972598B |
0.393 |
|
| 1997 |
Figueirido F, Del Buono GS, Levy RM. On Finite-Size Corrections to the Free Energy of Ionic Hydration The Journal of Physical Chemistry B. 101: 5622-5623. DOI: 10.1021/Jp970882X |
0.331 |
|
| 1997 |
Jin D, Figueirido F, Montelione GT, Levy RM. Impact of the Precision in NMR Relaxation Measurements on the Interpretation of Protein Dynamics Journal of the American Chemical Society. 119: 6923-6924. DOI: 10.1021/Ja970947+ |
0.313 |
|
| 1996 |
Fadel AR, Jin DQ, Montelione GT, Levy RM. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor. Journal of Biomolecular Nmr. 6: 221-6. PMID 8589611 DOI: 10.1007/Bf00211787 |
0.303 |
|
| 1996 |
Figueirido F, Del Buono GS, Levy RM. Prediction of pKaShifts without Truncation of Electrostatic Interactions: An Explicit Solvent Calculation for Succinic Acid The Journal of Physical Chemistry. 100: 6389-6392. DOI: 10.1021/Jp9600524 |
0.392 |
|
| 1995 |
Suri AK, Levy RM. A Relaxation-Matrix Analysis of Distance-Constraint Ranges for NOEs in Proteins at Long Mixing Times Journal of Magnetic Resonance, Series B. 106: 24-31. PMID 7850172 DOI: 10.1006/Jmrb.1995.1004 |
0.311 |
|
| 1995 |
Del Buono GS, Figueirido FE, Levy RM. Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme. Proteins. 20: 85-97. PMID 7824525 DOI: 10.1002/Prot.340200109 |
0.431 |
|
| 1995 |
Figueirido F, Del Buono GS, Levy RM. On finite‐size effects in computer simulations using the Ewald potential The Journal of Chemical Physics. 103: 6133-6142. DOI: 10.1063/1.470721 |
0.309 |
|
| 1995 |
Ding Y, Bernardo DN, Krogh-Jespersen K, Levy RM. Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials The Journal of Physical Chemistry. 99: 11575-11583. DOI: 10.1021/J100029A040 |
0.37 |
|
| 1994 |
Chen Y, Suri AK, Kominos D, Sanyal G, Naylor AM, Pitzenberger SM, Garsky VM, Levy RM, Baum J. Three-dimensional structure of echistatin and dynamics of the active site. Journal of Biomolecular Nmr. 4: 307-24. PMID 8019139 DOI: 10.1007/Bf00179342 |
0.379 |
|
| 1994 |
Figueirido F, Del Buono GS, Levy RM. Molecular mechanics and electrostatic effects. Biophysical Chemistry. 51: 235-41. PMID 7919034 DOI: 10.1016/0301-4622(94)00044-1 |
0.332 |
|
| 1994 |
Matubayasi N, Reed LH, Levy RM. Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute The Journal of Physical Chemistry. 98: 10640-10649. DOI: 10.1021/J100092A040 |
0.309 |
|
| 1994 |
Bernardo DN, Ding Y, Krogh-Jespersen K, Levy RM. An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields The Journal of Physical Chemistry. 98: 4180-4187. DOI: 10.1021/J100066A043 |
0.346 |
|
| 1993 |
Smith-Brown MJ, Kominos D, Levy RM. Global folding of proteins using a limited number of distance constraints. Protein Engineering. 6: 605-14. PMID 7694274 DOI: 10.1093/Protein/6.6.605 |
0.325 |
|
| 1992 |
Kitchen DB, Reed LH, Levy RM. Molecular dynamics simulation of solvated protein at high pressure. Biochemistry. 31: 10083-93. PMID 1382594 DOI: 10.1021/Bi00156A031 |
0.313 |
|
| 1992 |
Figueirido FE, Levy RM. Vibrational relaxation and Bloch–Redfield theory The Journal of Chemical Physics. 97: 703-706. DOI: 10.1063/1.463566 |
0.309 |
|
| 1992 |
Kominos D, Suri AK, Kitchen DB, Bassolino D, Levy RM. Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data Journal of Magnetic Resonance (1969). 97: 398-410. DOI: 10.1016/0022-2364(92)90325-2 |
0.778 |
|
| 1991 |
Levy RM, Belhadj M, Kitchen DB. Gaussian fluctuation formula for electrostatic free‐energy changes in solution The Journal of Chemical Physics. 95: 3627-3633. DOI: 10.1063/1.460813 |
0.302 |
|
| 1991 |
Levy RM, Westbrook JD, Kitchen DB, Krogh-Jespersen K. Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water The Journal of Physical Chemistry. 95: 6756-6758. DOI: 10.1021/J100171A005 |
0.397 |
|
| 1991 |
Belhadj M, Alper HE, Levy RM. Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions Chemical Physics Letters. 179: 13-20. DOI: 10.1016/0009-2614(91)90284-G |
0.362 |
|
| 1990 |
Kominos D, Bassolino DA, Levy RM, Pardi A. Analysis of side-chain conformational distributions in neutrophil peptide-5 NMR structures. Biopolymers. 29: 1807-22. PMID 2207287 DOI: 10.1002/Bip.360291412 |
0.782 |
|
| 1990 |
Metzler WJ, Wang C, Kitchen DB, Levy RM, Pardi A. Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and constrained molecular dynamics. Journal of Molecular Biology. 214: 711-36. PMID 2167379 DOI: 10.1016/0022-2836(90)90288-W |
0.348 |
|
| 1990 |
Levy RM, Kitchen DB, Blair JT, Krogh-Jespersen K. Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water The Journal of Physical Chemistry. 94: 4470-4476. DOI: 10.1021/J100374A023 |
0.353 |
|
| 1990 |
Blair JT, Levy RM, Krogh-Jespersen K. Molecular mechanics parameters for electronically excited states: The (n, π*) singlet state of formaldehyde Chemical Physics Letters. 166: 429-436. DOI: 10.1016/0009-2614(90)85056-I |
0.325 |
|
| 1990 |
Kitchen DB, Hirata F, Westbrook JD, Levy R, Kofke D, Yarmush M. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water Journal of Computational Chemistry. 11: 1169-1180. DOI: 10.1002/Jcc.540111009 |
0.351 |
|
| 1990 |
Perahia D, Levy RM, Karplus M. Motions of an ?-helical polypeptide: Comparison of molecular and harmonic dynamics Biopolymers. 29: 645-677. DOI: 10.1002/Bip.360290402 |
0.638 |
|
| 1989 |
Levy RM, Bassolino DA, Kitchen DB, Pardi A. Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. Biochemistry. 28: 9361-72. PMID 2611235 DOI: 10.1021/Bi00450A017 |
0.788 |
|
| 1989 |
Alper HE, Levy RM. Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models The Journal of Chemical Physics. 91: 1242-1251. DOI: 10.1063/1.457198 |
0.33 |
|
| 1989 |
Blair JT, Krogh-Jespersen K, Levy RM. Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water Journal of the American Chemical Society. 111: 6948-6956. DOI: 10.1021/Ja00200A009 |
0.331 |
|
| 1989 |
Blair JT, Westbrook JD, Levy RM, Krogh-Jespersen K. Simple models for solvation effects on electronic transition energies: Formaldehyde and water Chemical Physics Letters. 154: 531-535. DOI: 10.1016/0009-2614(89)87146-5 |
0.355 |
|
| 1988 |
Bassolino DA, Hirata F, Kitchen DB, Kominos D, Pardi A, Levy RM. Determination of Protein Structures in Solution Using Nmr Data and Impact The International Journal of Supercomputing Applications. 2: 41-61. DOI: 10.1177/109434208800200204 |
0.791 |
|
| 1988 |
Hirata F, Redfern P, Levy RM. Viewing the born model for ion hydration through a microscope International Journal of Quantum Chemistry. 34: 179-190. DOI: 10.1002/Qua.560340716 |
0.334 |
|
| 1987 |
Westhof E, Chevrier B, Gallion SL, Weiner PK, Levy RM. Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. Journal of Molecular Biology. 191: 699-712. PMID 3806679 DOI: 10.1016/0022-2836(86)90454-7 |
0.349 |
|
| 1986 |
Kuriyan J, Petsko GA, Levy RM, Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. Journal of Molecular Biology. 190: 227-54. PMID 3795269 DOI: 10.1016/0022-2836(86)90295-0 |
0.625 |
|
| 1986 |
Levy RM. Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X‐Ray Refinement Annals of the New York Academy of Sciences. 482: 24-43. PMID 3471107 DOI: 10.1111/J.1749-6632.1986.Tb20934.X |
0.378 |
|
| 1986 |
Rojas OL, Levy RM, Szabo A. Corrections to the quasiharmonic approximation for evaluating molecular entropies The Journal of Chemical Physics. 85: 1037-1043. DOI: 10.1063/1.451296 |
0.364 |
|
| 1986 |
Weiner PK, Gallion SL, Westhof E, Levy RM. Visualization of energetics and conformations from molecular computer simulations Journal of Molecular Graphics. 4: 203-207. DOI: 10.1016/0263-7855(86)80041-8 |
0.405 |
|
| 1986 |
Levy RM. Using Macromolecular Dynamics Simulations to Interpret Experiments Israel Journal of Chemistry. 27: 173-179. DOI: 10.1002/Ijch.198600026 |
0.375 |
|
| 1985 |
Levy RM, Sheridan RP, Keepers JW, Dubey GS, Swaminathan S, Karplus M. Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. Biophysical Journal. 48: 509-18. PMID 3840041 DOI: 10.1016/S0006-3495(85)83806-6 |
0.516 |
|
| 1984 |
Levy RM, Srinivasan AR, Olson WK, McCammon JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers. 23: 1099-112. PMID 6733249 DOI: 10.1002/Bip.360230610 |
0.453 |
|
| 1984 |
Levy RM, Karplus M, Kushick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix Macromolecules. 17: 1370-1374. DOI: 10.1021/Ma00137A013 |
0.64 |
|
| 1984 |
Olejniczak ET, Dobson CM, Karplus M, Levy RM. Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme Journal of the American Chemical Society. 106: 1923-1930. DOI: 10.1021/Ja00319A004 |
0.487 |
|
| 1984 |
OLEJNICZAK ET, DOBSON CM, KARPLUS M, LEVY RM. ChemInform Abstract: MOTIONAL AVERAGING OF PROTON NUCLEAR OVERHAUSER EFFECTS IN PROTEINS. PREDICTIONS FROM A MOLECULAR DYNAMICS SIMULATION OF LYSOZYME Chemischer Informationsdienst. 15. DOI: 10.1002/chin.198427055 |
0.412 |
|
| 1982 |
Sheridan RP, Levy RM, Salemme FR. alpha-Helix dipole model and electrostatic stabilization of 4-alpha-helical proteins. Proceedings of the National Academy of Sciences of the United States of America. 79: 4545-4549. PMID 6956878 DOI: 10.1073/Pnas.79.15.4545 |
0.329 |
|
| 1982 |
Levy RM, Dobson CM, Karplus M. Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects. Biophysical Journal. 39: 107-13. PMID 6179550 DOI: 10.1016/S0006-3495(82)84496-2 |
0.489 |
|
| 1982 |
Lipari G, Szabo A, Levy RM. Protein dynamics and NMR relaxation: comparison of simulations with experiment Nature. 300: 197-198. DOI: 10.1038/300197A0 |
0.393 |
|
| 1982 |
LEVY RM, KARPLUS M, WOLYNES PG. ChemInform Abstract: NMR RELAXATION PARAMETERS IN MOLECULES WITH INTERNAL MOTION: EXACT LANGEVIN TRAJECTORY RESULTS COMPARED WITH SIMPLIFIED RELAXATION MODELS Chemischer Informationsdienst. 13. DOI: 10.1002/chin.198203044 |
0.377 |
|
| 1981 |
Levy RM, Karplus M, Wolynes PG. NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models Journal of the American Chemical Society. 103: 5998-6011. DOI: 10.1021/Ja00410A002 |
0.455 |
|
| 1981 |
Levy RM, Karplus M, McCammon JA. Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging Journal of the American Chemical Society. 103: 994-996. DOI: 10.1021/Ja00394A072 |
0.528 |
|
| 1981 |
LEVY RM, KARPLUS M, MCCAMMON JA. ChemInform Abstract: INCREASE OF CARBON-13 NMR RELAXATION TIMES IN PROTEINS DUE TO PICOSECOND MOTIONAL AVERAGING Chemischer Informationsdienst. 12. DOI: 10.1002/chin.198122050 |
0.475 |
|
| 1981 |
Pear MR, Northrup SH, McCammon JA, Karplus M, Levy RM. Correlated helix-coil transitions in polypeptides Biopolymers. 20: 629-632. DOI: 10.1002/Bip.1981.360200314 |
0.51 |
|
| 1980 |
Levy RM, Karplus M, McCammon JA. Molecular dynamics studies of NMR relaxation in proteins. Biophysical Journal. 32: 628-30. PMID 19431400 DOI: 10.1016/S0006-3495(80)84998-8 |
0.572 |
|
| 1980 |
McCammon JA, Northrup SH, Karplus M, Levy RM. Helix-coil transitions in a simple polypeptide model Biopolymers. 19: 2033-2045. DOI: 10.1002/Bip.1980.360191108 |
0.594 |
|
| 1979 |
Levy RM, Karplus M, Andrew McCammon J. Diffusive langevin dynamics of model alkanes Chemical Physics Letters. 65: 4-11. DOI: 10.1016/0009-2614(79)80114-1 |
0.453 |
|
| 1979 |
Levy RM, Karplus M. Vibrational approach to the dynamics of an ?-helix Biopolymers. 18: 2465-2495. DOI: 10.1002/Bip.1979.360181008 |
0.47 |
|
| 1976 |
Levy RM, Kushmerick MJ. Induction of contractile activity by rigor complexes in myofibrils. Biochemical and Biophysical Research Communications. 76: 512-9. PMID 141286 DOI: 10.1016/0006-291X(77)90754-9 |
0.532 |
|
| 1976 |
Levy RM, Umazume Y, Kushmerick MJ. Ca2+ dependence of tension and ADP production in segments of chemically skinned muscle fibers. Biochimica Et Biophysica Acta. 430: 352-65. PMID 132189 DOI: 10.1016/0005-2728(76)90091-8 |
0.517 |
|
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