Publications


  1. Emilio Gallicchio. Alchemical Response Parameters from an Analytical Model of Molecular Binding. arXiv:1707.00769 

  2. Baofeng Zhang, Denise Kilburg, Peter Eastman, Vijay S. Pande, Emilio Gallicchio. Efficient Gaussian Density Formulation of Volume and Surface Areas of Macromolecules on Graphical Processing Units. J. Comp. Chem., 38, 740-752 (2017). doi:10.1002/jcc.24745 pdf of submitted manuscript

  3. Baofeng Zhang, Michael P. D'Erasmo, Ryan P. Murelli, Emilio Gallicchio. Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase. ACS Omega. 1, 435-447 (2016). doi:10.1021/acsomega.6b00123 pdf of submitted manuscript

  4. Rajat Kumar Pal, Kamran Haider, Divya Kaur, William Flynn, Junchao Xia,  Ronald M Levy, Tetiana Taran,* Lauren Wickstrom,  Tom Kurtzman, Emilio Gallicchio. A Combined Treatment of Hydration and Dynamical Effects for the Modeling of Host-Guest Binding Thermodynamics: The SAMPL5 Blinded Challenge. J. Comp. Aided. Mol. Des. 31, 29 (2016). *Undergraduate student. Free access on SpringerNature doi:10.1007/s10822-016-9956-6

  5. Denise Kilburg and Emilio Gallicchio. Recent Advances in Computational Models for the Study Protein-Peptide Interactions. Adv. Prot. Chem. Struct. Biol. 105, 27-57 (2016). doi:10.1016/bs.apcsb.2016.06.002 pdf of submitted manuscript 

  6. Nanjie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mantes, Emilio Gallicchio and Ronald M. Levy. Blind Predictions of Protein-Ligand Binding Affinities by Large-Scale BEDAM Free Energy Calculations: the D3R Grand Challenge 2015. J. Comp. Aided. Mol. Des. 30.9 , 743-751 (2016). doi:10.1007/s10822-016-9952-x

  7. Ryan P Murelli, Michael P D'Erasmo, Danielle R Hirsch, C Meck, T Masaoka, JA Wilson, Baofeng Zhang, Rajat K Pal, Emilio Gallicchio, John A Beutler, Stuart F Le Grice. Synthetic α-hydroxytropolones as inhibitors of HIV reverse transcriptase ribonuclease H activity. MedChemComm. 7, 1783-1788 (2016). doi:10.1039/C6MD00238B

  8. A Mentes, NJ Deng, RSK Vijayan, J Xia, E Gallicchio, RM Levy. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation. J. Chem. Theory Comput. 12, 2459-2470 (2016). doi:10.1021/acs.jctc.6b00134

  9. Lauren Wickstrom, Nanjie Deng, Peng He, Ahmet Mentes ,Crystal Nguyen, Michael K. Gilson, Tom Kurtzman, Emilio Gallicchio, and Ronald M. Levy. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. J. Molecular Recognition, 29.1, 10-21 (2016). doi:10.1002/jmr.2489

  10. Bin W Zhang, Wei Dai, Emilio Gallicchio, Peng He, Junchao Xia, Zhiqiang Tan, Ronald M Levy. Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit. J. Phys. Chem. B, 120, 8289–8301 (2016). doi:10.1021/acs.jpcb.6b02015

  11. Emilio Gallicchio, Junchao Xia, William F Flynn, Baofeng Zhang, Sade Samlalsingh,* Ahmet Mentes, Ronald M Levy. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing. Computer Physics Communications, 196, 236–246 (2015). doi:10.1016/j.cpc.2015.06.010 PubMed *Undergraduate student.

  12. Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy. Large Scale Asynchronous and Distributed Multi-Dimensional Replica Exchange Molecular Simulations and Efficiency Analysis. J. Comp. Chem, 36, 1772-1785 (2015). doi:10.1002/jcc.23996

  13. Daniele Di Marino, Ilda D'Annessa, Holly Tancredi,* Claudia Bagni, Emilio Gallicchio. A Unique Binding Mode of the Eukaryotic Translation Initiation Factor 4E for Guiding the Design of Novel Peptide Inhibitors. Protein Science, 24, 1370-1382 (2015). *Undergraduate student. doi:10.1002/pro.2708 Predicted structure of the eIF4E/CYFIP1p complex: pdb

  14. Deng, Nan-jie; Forli, Stefano; He, Peng; Perryman, Alex; Wickstrom, Lauren; Vijayan, Suyambu Kesava Vijayan; Tiefenbrunn, Theresa; Stout, C.; Gallicchio, Emilio; Olson, Arthur; Levy, Ronald M. Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. J. Phys. Chem B 119, 976–988 (2015). doi:10.1021/jp506376z

  15. Emilio Gallicchio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi Pethe, Jie Zhu and Ronald M Levy. BEDAM Binding Free Energy Predictions for the SAMPL4 Octa-Acid Host Challenge. J. Comp. Aided Mol. Des. 29, 315-325 (2015), doi:10.1007%2Fs10822-014-9795-2

  16. Emilio Gallicchio, Nanjie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson and Ronald M. Levy. Virtual Screening of Integrase Inhibitors by Large Scale Binding Free Energy Calculations: the SAMPL4 Challenge. J Comp Aided Mol Design, 28, 475-490 (2014). doi:10.1007/s10822-014-9711-9

  17. Guohua Yi, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, Gail Ferstandig Arnold. Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses.  PLoS ONE 8(9), e72205 (2013). doi:10.1371/journal.pone.0072205

  18. Brian K Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M York, Ronald M Levy, Shantenu Jha. A framework for flexible and scalable replica-exchange on production distributed CI. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment. ACM (2013). doi:10.1145/2484762.2484830

  19. 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. J Chem Theory Comput, 9, 3136–3150 (2013). doi:10.1021/ct400003r

  20. Tan Z, Gallicchio E, Lapelosa M, Levy RM. Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys, 136, 144102 (2012).pdf  doi:10.1063/1.3701175

  21. 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 (2012).doi:10.4236/cmb.2012.21002

  22. Gallicchio E, Levy RM. Prediction of SAMPL3 Host-Guest Affinities with the Binding Energy Distribution Analysis Method (BEDAM). J Comp Aided Mol Design, 26, 505-516 (2012).doi:10.1007/s10822-012-9552-3

  23. Lapelosa M, Gallicchio E, Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput, 8, 44-60 (2012).doi:10.1021/ct200684b JCTC Most Read Article Q1 2012

  24. Bell JA, Cao Y, Gunn, JR, Day T, Gallicchio E, Zhou Z, Levy RM and Farid R. PrimeX and the Schrödinger Computational Chemistry Suite of Programs. International Tables for Crystallography, 534-538 (2012).html

  25. Wickstrom L, Gallicchio E and Levy RM. The Linear Interaction Energy Method for the Prediction of Stability Changes Upon Mutation. Proteins, 80, 111-125 (2011). doi:10.1002/prot.23168

  26. Emilio Gallicchio and Ronald M Levy, Recent Theoretical and Computational Advances for Modeling Protein-Ligand Binding Affinities. Advances in Protein Chemistry and Structural Biology, 85, 27-80, (2011). PubMed doi:10.1016/B978-0-12-386485-7.00002-8

  27. Deng, N., W. Zheng, E. Gallicchio, and R.M. Levy. Insights into the Dynamics of HIV-1 Protease: a Kinetic Network Model Constructed from Atomistic Simulations. J. Am. Chem. Soc., 133, 9387-9894 (2011). PubMed | doi:10.1021/ja2008032

  28. Zheng, W., E. Gallicchio, N. Deng, M. Andrec, and R.M. Levy. Kinetic Network Study of the Diversity and Temperature Dependence of TRP-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations. J. Phys. Chem. B, 115, 1512-1523 (2011). PubMed | doi:10.1021/jp1089596

  29. Gallicchio E and Levy RM. Advances in all atom sampling methods for modeling protein-ligand binding affinities . Curr Op Struct Biol, 21, 161-166 (2011). PubMed | doi:10.1016/j.sbi.2011.01.010

  30. Gallicchio E, Lapelosa M, Levy RM. Binding energy distribution analysis method (BEDAM) for estimation of protein-ligand binding affinities. J Chem Theory Comput, 6, 2961-2977 (2010). PubMed | doi:10.1021/ct1002913

  31. Lapelosa M, Ferstandig Arnold G, Gallicchio E, Arnold E, and Levy RM. Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes. J Mol Biol, 397, 752-766 (2010). PubMed | doi:10.1016/j.jmb.2010.01.064

  32. Okumura H, Gallicchio E, and Levy RM. Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comp Chem, 31, 1357-1367 (2009). PubMed | doi:10.1002/jcc.21419

  33. Gallicchio E, Paris K, and Levy RM. The AGBNP2 Implicit Solvent Model. J Chem Theory Comput, 5, 2544-2564 (2009). PubMed | doi:10.1021/ct900234u

  34. Zheng, W., M. Andrec, E. Gallicchio, and R.M. Levy. Recovering Kinetics from a Simplified Protein-Folding Model Using Replica Exchange Simulations, a Kinetic Network and Effective Stochastic Dynamics. J. Phys. Chem. B., 113, 11702-11709 (2009). PubMed | doi:10.1021/jp900445t

  35. Frenkel, Y.V., E. Gallicchio, K. Das, R.M. Levy, and E. Arnold. Molecular dynamics study of non-nucleoside HIV-1 RT inhibitor TMC278/rilpivirine aggregates: correlation between amphiphilic properties of the drug and oral bioavailability. J. Med. Chem., 52, 5896-5905 (2009). PubMed | doi:10.1021/jm900282z

  36. Lapelosa, M., E. Gallicchio, G. Ferstandig Arnold, E. Arnold and R.M. Levy. In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J. Mol. Biol., 385, 675-691 (2009). PubMed | doi:10.1016/j.jmb.2008.10.089

  37. Felts, A.K., M. Andrec, E. Gallicchio, and R.M. Levy. Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models, in "Water and Biomolecules - Physical Chemistry of Life Phenomena", Springer Science (2008).

  38. Felts, A.K., K. Paris, E. Gallicchio, R.A. Friesner, and R.M. Levy. Predicting Long Loops with the AGBNP Implicit Solvent Model using Hierarchical Torsion Angle Sampling and Protein Local Optimization. J. Chem. Theor. Comp., 4, 855-858 (2008). PubMed | doi:10.1021/Fct800051k

  39. Zheng, W., M. Andrec, E. Gallicchio, and R.M. Levy. Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding. J. Phys. Chem. B, 112, 6083-6093 (2008). PubMed | doi:10.1021/jp076377+

  40. Gallicchio, E., R.M. Levy, and M. Parashar. Asynchronous Replica Exchange for Molecular Simulations. J. Comp. Chem., 29, 788-794 (2008). PubMed | doi:10.1002/jcc.20839

  41. Knight, J.L., Z. Zhou, E. Gallicchio, D.M. Himmel, R.A. Friesner, E. Arnold, and R.M. Levy. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion angle sampling. Acta. Cryst., D64, 383-396 (2008). PubMed | doi:10.1107/S090744490800070X

  42. Zheng, W., M. Andrec, E. Gallicchio, and R.M. Levy. Simulating replica exchange simulations of protein folding with a kinetic network model. Proc. Natl. Acad. Sci. USA, 104, 15340-15345 (2007). PubMed | doi:10.1073/pnas.0704418104

  43. Krishna Pratap Ravindranathan, Emilio Gallicchio, Ann E. McDermott, and Ronald M. Levy Conformational Dynamics of Substrate in the Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from NMR Order Parameters. J. Am. Chem. Soc. 129, 474-475 (2007). doi:10.1021/ja0672371

  44. Su, Y., E. Gallicchio, K. Das, E. Arnold, and R.M. Levy. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase, J. Chem. Theory Comput., 3, 256-277 (2007). doi:10.1021/ct600258e

  45. Ravindranathan, K.P., E. Gallicchio, R.A. Friesner, A.E. McDermott, and R.M. Levy. Conformational equilibrium of cytochrome P450 BM-3 complexed with N-Palmitoylglycine: A replica exchange molecular dynamics study. J. Am. Chem. Soc., 128, 5786-5791 (2006). doi:10.1021/ja058465i

  46. Zhang, L., M. Parashar, E. Gallichio and R.M. Levy. Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. Proceedings of the 35th International Conference on Parallel Processing (ICPP 2006), Columbus, OH, USA, IEEE Computer Society Press, pp. 127 - 134, August 2006. doi:10.1109/ICPP.2006.63

  47. Ravindranathan, K.P., E. Gallicchio, and R.M. Levy. Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose Binding Protein. J. Mol. Biol., 353, 196-210 (2005). doi:10.1016/j.jmb.2005.08.009

  48. Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts, T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky, L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752 (2005). doi:10.1002/jcc.20292

  49. Andrec, M., A.K. Felts, E. Gallicchio, and R.M. Levy. Protein Folding Pathways from Replica Exchange Simulations and a Kinetic Network Model. Proceedings Natl. Acad. Sci. USA, 102, 6801-6806 (2005). doi:10.1073/pnas.0408970102

  50. Gallicchio, E., M. Andrec, A.K. Felts, and R.M. Levy. Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths. J. Phys. Chem. B, 109, 6722-6731 (2005). doi:10.1021/jp045294f

  51. Felts, A.K., Y. Harano, E. Gallicchio, R.M. Levy. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGNP implicit solvent model. PROTEINS: Structure, Function, and Bioinformatics, 56,310-321 (2004). doi:10.1002/prot.20104

  52. Y. Su and E. Gallicchio, 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. 109:251-260 (2004).doi:10.1016/j.bpc.2003.11.007

  53. Gallicchio E., and R.M. Levy. AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling, J. Comp. Chem. 25, 479-499 (2004).doi:10.1002/jcc.10400

  54. R. M. Levy, L. Y. Zhang, E. Gallicchio, A. K. Felts, On the Non-Polar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy, J. Am. Chem. Soc., 125, 9523-9530 (2003).

  55. Felts, A.K., E. Gallicchio, A. Wallqvist, and R.M. Levy. 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, 404-422 (2002).

  56. E. Gallicchio, L.Y. Zhang, and R.M. Levy. The SGB/NP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and Novel Non-Polar Hydration Free Energy Estimators. J. Comp. Chem., 23, 517-529 (2002).

  57. Wallqvist, A., E. Gallicchio, A.K. Felts, and R.M. Levy. Detecting Native Protein Folds Among Large Decoy Sets With the OPLS All-Atom Potential and Surface Generalized Born Solvent Model, in "Computational Methods for Protein Folding: A Special Volume of Advances in Chemical Physics," Vol. 120, R. Friesner, editor, I. Prigogine and S.A. Rice, series editors, John Wiley & Sons, 459-486 (2002).

  58. Wallqvist, A., E. Gallicchio, and R.M. Levy. A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties. J. Phys. Chem.,105, 6745-6753 (2001).

  59. Felts, A.K., A. Wallqvist, E. Gallicchio, D. Bassolino, S.R. Krystek and R.M. Levy. Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model, in "Lecture Notes in Computational Science and Engineering (LNCSE)", Vol. 24, Springer-Verlag, Berlin, 2002.

  60. Chernyavsky, B., E. Gallicchio, D. Knight, R. Levy, and A. Page. The Rutgers Computational Grid: A Distributed Linux PC Cluster.   Cluster Computing (2002)

  61. Zhang, L., E. Gallicchio, R. Friesner, and R.M. Levy. Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations. J. Comp. Chem., 22, 591-607 (2001).

  62. Gallicchio, E., M. Kubo, and R.M. Levy. Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation. J. Phys. Chem., 104, 6271-6285 (2000).

  63. Zhang, L., E. Gallicchio, and R.M. Levy. Implicit Solvent Models for Protein-Ligand Binding: Insights Based on Explicit Solvent Simulations. AIP Conference Proceedings (Simulation and Theory of Electrostatic Interactions in Solutions), 492, 451-472 (1999).

  64. Matubayasi, N., E. Gallicchio, and R.M. Levy. On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models. J. Chem. Phys., 109, 4864-4872 (1998).

  65. Gallicchio, E., M.M. Kubo, and R.M. Levy. Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited. J. Am. Chem Soc., 120, 4526-4527 (1998).

  66. Levy, R.M., and E. Gallicchio. 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, 531-567 (1998).

  67. Kubo, M.M., E. Gallicchio, and R.M. Levy. Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides. J. Phys. Chem., 101, 10527-10534 (1997).

  68. E. Gallicchio, S. A. Egorov and B. J. Berne. On the Application of Numerical Analytic Continuation Methods to the Study of Quantum Mechanical Vibrational Relaxation Processes, J. Chem. Phys., 109, 7745 (1998).

  69. S. A. Egorov, E. Gallicchio, B. J. Berne. The Simulation of the Electronic Absorption Spectrum of a Chromophore Coupled to a Condensed Phase Environment: Maximum Entropy Versus Singular Value Decomposition Approaches, J. Chem. Phys., 107 (22), (1997).

  70. E. Gallicchio, B. J. Berne. On the Calculation of Dynamical Properties of Solvated Electrons by Maximum Entropy Analytic Continuation of Path Integral Monte Carlo data, J. Chem. Phys., 105, 7064 (1996).

  71. F. Battaglia, T.F. George, E. Gallicchio. " Lezioni di Fisica Classica e Quantistica " , CEDAM, Padova, Italy, 1996. pdf

  72. E. Gallicchio, B. J. Berne, 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, J. Chem. Phys., 101, 9909 (1994).

  73. F. Battaglia, E. Gallicchio.Thermodynamic Analysis of the 1x ∞ vs 2x∞ Lattice Gases as Models for Molecular Adsorption on Surfaces, J. Phys. Chem., 97, 6530 (1993).

  74. E. Gallicchio, F. Battaglia.FORTRAN Routine to Compute Born-Oppenheimer Potential Energy Curves Directly from Spectroscopic Data, J. Comput. Chem., 14, 579 (1993).

  75. Ph.D. thesis: " Quantum Dynamics in Condensed Phases by Maximum Entropy Analytic Continuation of Euclidean Time Path Integrals ", Graduate School of Arts and Sciences, Columbia University, New York, 1996. pdf