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Emilio Gallicchio - Publications

Affiliations: 
2013- Brooklyn College of CUNY 
Area:
Models of Molecular Recognition
Website:
http://compmolbiophysbc.org

55 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
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  0.48
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  0.52
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  0.52
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  0.92
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  0.52
2017 Zhang B, Kilburg D, Eastman P, Pande VS, Gallicchio E. Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. Journal of Computational Chemistry. PMID 28160511 DOI: 10.1002/jcc.24745  0.36
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  0.48
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  0.92
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  0.36
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  0.88
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  0.88
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  0.88
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  0.88
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  0.92
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  0.92
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.92
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  0.88
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  0.92
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  0.92
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  0.92
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  0.88
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.88
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  0.92
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  0.92
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  0.88
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  0.88
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+  0.92
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  0.88
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  0.92
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  0.92
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  0.88
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  0.88
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  0.92
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  0.88
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  0.92
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  0.92
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  0.92
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  0.36
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  0.92
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  0.92
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  0.92
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  0.92
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