| Year |
Citation |
Score |
| 2024 |
Sabanés Zariquiey F, Galvelis R, Gallicchio E, Chodera JD, Markland TE, De Fabritiis G. Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. Journal of Chemical Information and Modeling. 64: 1481-1485. PMID 38376463 DOI: 10.1021/acs.jcim.3c02031 |
0.701 |
|
| 2024 |
Zariquiey FS, Galvelis R, Gallicchio E, Chodera JD, Markland TE, de Fabritiis G. Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials. Arxiv. PMID 38351937 |
0.701 |
|
| 2024 |
Khuttan S, Gallicchio E. What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling. Journal of Chemical Theory and Computation. 20: 1489-1501. PMID 38252868 DOI: 10.1021/acs.jctc.3c01250 |
0.377 |
|
| 2023 |
Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry. B. PMID 38154096 DOI: 10.1021/acs.jpcb.3c06662 |
0.613 |
|
| 2023 |
Chen L, Wu Y, Wu C, Silveira A, Sherman W, Xu H, Gallicchio E. Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. Journal of Chemical Information and Modeling. PMID 38147877 DOI: 10.1021/acs.jcim.3c01705 |
0.671 |
|
| 2023 |
Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. Arxiv. PMID 37986730 |
0.612 |
|
| 2023 |
Khuttan S, Azimi S, Wu JZ, Dick S, Wu C, Xu H, Gallicchio E. Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host-guest SAMPL9 blinded challenge. Physical Chemistry Chemical Physics : Pccp. PMID 37676233 DOI: 10.1039/d3cp02125d |
0.717 |
|
| 2023 |
Sabanés Zariquiey F, Pérez A, Majewski M, Gallicchio E, De Fabritiis G. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. Journal of Chemical Information and Modeling. 63: 2438-2444. PMID 37042797 DOI: 10.1021/acs.jcim.3c00178 |
0.398 |
|
| 2023 |
Zariquiey FS, Pérez A, Majewski M, Gallicchio E, Fabritiis G. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. Arxiv. PMID 36994153 |
0.398 |
|
| 2022 |
Gallicchio E. Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria. Methods in Molecular Biology (Clifton, N.J.). 2405: 303-334. PMID 35298820 DOI: 10.1007/978-1-0716-1855-4_15 |
0.377 |
|
| 2022 |
Wickstrom L, Gallicchio E, Chen L, Kurtzman T, Deng N. Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model. Physical Chemistry Chemical Physics : Pccp. PMID 35212338 DOI: 10.1039/d1cp05075c |
0.782 |
|
| 2022 |
Azimi S, Wu JZ, Khuttan S, Kurtzman T, Deng N, Gallicchio E. Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge. Journal of Computer-Aided Molecular Design. 36: 63-76. PMID 35059940 DOI: 10.1007/s10822-021-00437-y |
0.78 |
|
| 2022 |
Azimi S, Khuttan S, Wu JZ, Pal RK, Gallicchio E. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. Journal of Chemical Information and Modeling. PMID 34990555 DOI: 10.1021/acs.jcim.1c01129 |
0.798 |
|
| 2021 |
Wu JZ, Azimi S, Khuttan S, Deng N, Gallicchio E. Alchemical Transfer Approach to Absolute Binding Free Energy Estimation. Journal of Chemical Theory and Computation. 17: 3309-3319. PMID 33983730 DOI: 10.1021/acs.jctc.1c00266 |
0.448 |
|
| 2021 |
Cordone P, Namballa HK, Muniz B, Pal RK, Gallicchio E, Harding WW. New tetrahydroisoquinoline-based DR ligands with an o-xylenyl linker motif. Bioorganic & Medicinal Chemistry Letters. 128047. PMID 33882273 DOI: 10.1016/j.bmcl.2021.128047 |
0.723 |
|
| 2021 |
Khuttan S, Azimi S, Wu JZ, Gallicchio E. Alchemical transformations for concerted hydration free energy estimation with explicit solvation. The Journal of Chemical Physics. 154: 054103. PMID 33557533 DOI: 10.1063/5.0036944 |
0.329 |
|
| 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 |
0.598 |
|
| 2020 |
Cruz J, Wickstrom L, Yang D, Gallicchio E, Deng N. Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. Journal of Chemical Theory and Computation. PMID 32101691 DOI: 10.1021/Acs.Jctc.9B01119 |
0.508 |
|
| 2019 |
Pal RK, Gallicchio E. Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations. The Journal of Chemical Physics. 151: 124116. PMID 31575187 DOI: 10.1063/1.5123154 |
0.778 |
|
| 2019 |
Pal RK, Gadhiya S, Ramsey S, Cordone P, Wickstrom L, Harding WW, Kurtzman T, Gallicchio E. Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes. Plos One. 14: e0222902. PMID 31568493 DOI: 10.1371/Journal.Pone.0222902 |
0.804 |
|
| 2019 |
He P, Sarkar S, Gallicchio E, Kurtzman T, Wickstrom L. The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin. The Journal of Physical Chemistry. B. PMID 31509409 DOI: 10.1021/Acs.Jpcb.9B07028 |
0.726 |
|
| 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 |
0.63 |
|
| 2019 |
Chakravorty A, Gallicchio E, Alexov E. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. Journal of Computational Chemistry. PMID 30698861 DOI: 10.1002/Jcc.25786 |
0.355 |
|
| 2018 |
Kilburg D, Gallicchio E. Analytical Model of the Free Energy of Alchemical Molecular Binding. Journal of Chemical Theory and Computation. PMID 30415541 DOI: 10.1021/Acs.Jctc.8B00967 |
0.506 |
|
| 2018 |
Gadhiya S, Cordone P, Pal RK, Gallicchio E, Wickstrom L, Kurtzman T, Ramsey S, Harding WW. New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif. Acs Medicinal Chemistry Letters. 9: 990-995. PMID 30344905 DOI: 10.1021/Acsmedchemlett.8B00229 |
0.777 |
|
| 2018 |
Kilburg D, Gallicchio E. Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes. Frontiers in Molecular Biosciences. 5: 22. PMID 29568737 DOI: 10.3389/Fmolb.2018.00022 |
0.501 |
|
| 2016 |
Murelli RP, D'Erasmo MP, Hirsch DR, Meck C, Masaoka T, Wilson JA, Zhang B, Pal RK, Gallicchio E, Beutler JA, Le Grice SF. Synthetic α-Hydroxytropolones as Inhibitors of HIV Reverse Transcriptase Ribonuclease H Activity. Medchemcomm. 7: 1783-1788. PMID 28093576 DOI: 10.1039/C6Md00238B |
0.701 |
|
| 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 |
0.78 |
|
| 2016 |
Zhang B, D'Erasmo MP, Murelli RP, Gallicchio E. Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase. Acs Omega. 1: 435-447. PMID 27713931 DOI: 10.1021/acsomega.6b00123 |
0.393 |
|
| 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 |
0.808 |
|
| 2016 |
Kilburg D, Gallicchio E. Recent Advances in Computational Models for the Study of Protein-Peptide Interactions. Advances in Protein Chemistry and Structural Biology. 105: 27-57. PMID 27567483 DOI: 10.1016/Bs.Apcsb.2016.06.002 |
0.336 |
|
| 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 |
0.652 |
|
| 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 |
0.557 |
|
| 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 |
0.662 |
|
| 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 |
0.423 |
|
| 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 |
0.81 |
|
| 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 |
0.524 |
|
| 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 |
0.566 |
|
| 2015 |
Di Marino D, D'Annessa I, Tancredi H, Bagni C, Gallicchio E. A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors. Protein Science : a Publication of the Protein Society. 24: 1370-82. PMID 26013047 DOI: 10.1002/Pro.2708 |
0.35 |
|
| 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 |
0.619 |
|
| 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 |
0.643 |
|
| 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 |
0.386 |
|
| 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 |
0.773 |
|
| 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 |
0.659 |
|
| 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 |
0.676 |
|
| 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 |
0.43 |
|
| 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 |
0.435 |
|
| 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 |
0.364 |
|
| 2012 |
Gallicchio E. Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. Computational Molecular Bioscience. 2: 7-22. PMID 22708073 DOI: 10.4236/cmb.2012.21002 |
0.432 |
|
| 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 |
0.621 |
|
| 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 |
0.676 |
|
| 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 |
0.659 |
|
| 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 |
0.521 |
|
| 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 |
0.499 |
|
| 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 |
0.618 |
|
| 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 |
0.634 |
|
| 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 |
0.541 |
|
| 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 |
0.659 |
|
| 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 |
0.542 |
|
| 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 |
0.592 |
|
| 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 |
0.417 |
|
| 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 |
0.518 |
|
| 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 |
0.565 |
|
| 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 |
0.486 |
|
| 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 |
0.512 |
|
| 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 |
0.512 |
|
| 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 |
0.572 |
|
| 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 |
0.529 |
|
| 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+ |
0.553 |
|
| 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 |
0.497 |
|
| 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 |
0.624 |
|
| 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 |
0.562 |
|
| 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 |
0.533 |
|
| 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 |
0.547 |
|
| 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 |
0.423 |
|
| 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 |
0.528 |
|
| 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, ... ... Gallicchio E, et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry. 26: 1752-80. PMID 16211539 DOI: 10.1002/Jcc.20292 |
0.635 |
|
| 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 |
0.61 |
|
| 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 |
0.526 |
|
| 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 |
0.523 |
|
| 2004 |
Su Y, Gallicchio E. The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions. Biophysical Chemistry. 109: 251-60. PMID 15110943 DOI: 10.1016/J.Bpc.2003.11.007 |
0.347 |
|
| 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 |
0.606 |
|
| 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 |
0.619 |
|
| 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 |
0.572 |
|
| 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 |
0.607 |
|
| 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 |
0.657 |
|
| 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 |
0.564 |
|
| 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 |
0.603 |
|
| 1998 |
Gallicchio E, Egorov SA, Berne BJ. On the application of numerical analytic continuation methods to the study of quantum mechanical vibrational relaxation processes Journal of Chemical Physics. 109: 7745-7755. DOI: 10.1063/1.477420 |
0.499 |
|
| 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 |
0.494 |
|
| 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 |
0.591 |
|
| 1997 |
Egorov SA, Gallicchio E, Berne BJ. The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus singular value decomposition approaches The Journal of Chemical Physics. 107: 9312-9318. DOI: 10.1063/1.475227 |
0.404 |
|
| 1997 |
Egorov SA, Gallicchio E, Berne BJ. The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus singular value decomposition approaches Journal of Chemical Physics. 107: 9312-9318. DOI: 10.1063/1.475227 |
0.496 |
|
| 1996 |
Gallicchio E, Berne BJ. On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data The Journal of Chemical Physics. 105: 7064-7078. DOI: 10.1063/1.472508 |
0.447 |
|
| 1996 |
Gallicchio E, Berne BJ. On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data Journal of Chemical Physics. 105: 7064-7078. DOI: 10.1063/1.472508 |
0.506 |
|
| 1994 |
Gallicchio E, Berne BJ. The absorption spectrum of the solvated electron in fluid helium by maximum entropy inversion of imaginary time correlation functions from path integral Monte Carlo simulations The Journal of Chemical Physics. 101: 9909-9918. DOI: 10.1063/1.467892 |
0.411 |
|
| 1994 |
Gallicchio E, Berne BJ. The absorption spectrum of the solvated electron in fluid helium by maximum entropy inversion of imaginary time correlation functions from path integral Monte Carlo simulations The Journal of Chemical Physics. 101: 9909-9918. DOI: 10.1063/1.467892 |
0.502 |
|
| 1993 |
Battaglia F, Gallicchio E. FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data Journal of Computational Chemistry. 14: 579-586. DOI: 10.1002/Jcc.540140511 |
0.328 |
|
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