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- Detailed Information
Emilio Gallicchio
Associate Professor
Chemistry
Location: 5315A Ingersoll Hall
Phone: 718.951.5000 x2249
Fax: 718.951.4607
Email:
Emilio Gallicchio's Web site
Emilio Gallicchio is the Levy-Kosminski Professor of Physical Chemistry at the Department of Chemistry and Biochemistry. He is a member of the Chemistry and Biochemistry graduate programs of CUNY. He has authored 98 research papers and monographs on topics ranging from quantum dynamics to HIV vaccine design, and he is the developer of several theoretical methods and software tools for the modeling of biological and chemical systems. Emilio Gallicchio received the NSF CAREER award in 2018. His current research is supported by the NIH.
Education:
Postdoctoral, Rutgers University - 2000 (Computational Molecular Biophysics)
Ph.D., Columbia University - 1996 (Chemical Physics)
M.Phil., Columbia University - 1995 (Chemical Physics)
M.A., Columbia University - 1992 (Chemical Physics)
B.A., University of Basilicata (Italy) - 1991 (Theoretical Chemistry)
Areas of Expertise:
Emilio Gallicchio's current research touches several areas of computational molecular biophysics and includes the study of the thermodynamics of protein-drug binding and conformational equilibria, solvation models development, and large-scale parallel and distributed computing.
Books and Publications
Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. J. Chem. Inf. Model. 63 (8), 2438-2444 (2023) (Books and Publications: Article (Peer-reviewed)) 2023
Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio. Performance and Analysis of the Alchemical Transfer Method for Binding Free Energy Predictions of Diverse Ligands. arXiv:2308.08671 (2023) (Books and Publications: Article (Other)) 2023
Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, Sebastian Dick, Chuanjie Wu, Huafeng Xu and Emilio Gallicchio. Taming Multiple Binding Poses in Alchemical Binding Free Energy Prediction: the β-cyclodextrin Host-Guest SAMPL9 Blinded Challenge. Phys. Chem. Chem. Phys., 2023,25, 24364-24376 (2023) (Books and Publications: Article (Peer-reviewed)) 2023
Lauren Wickstrom, Emilio Gallicchio, Lieyang Chen, Tom Kurtzman and Nanjie Deng. Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model. Physical Chemistry Chemical Physics 24, 6037-6052 (2022). (Books and Publications: Article (Peer-reviewed)) 2022
Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat K. Pal, and Emilio Gallicchio. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. J. Chem. Inf. Model. 62, 309 (2022). (Books and Publications: Article (Peer-reviewed)) 2022
Emilio Gallicchio. Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria. Methods in Molecular Biology, Computational Peptide Science: Methods and Protocols, Springer Nature, edited by Thomas Simonson (2021). (Books and Publications: Book Chapter) 2021
Joe Z. Wu, Solmaz Azimi, Sheenam Khuttan, Nanjie Deng, and Emilio Gallicchio. Alchemical Transfer Approach to Absolute Binding Free Energy Estimation. J. Chem. Theory and Comput. 17, 3306 (2021) (Books and Publications: Article (Peer-reviewed)) 2021
Pierpaolo Cordone, Hari K. Namballa, Bryant Muniz, Rajat K. Pal, Emilio Gallicchio, and Wayne Harding. New tetrahydroisoquinoline-based D3R ligands with an o-xylenyl linker motif. Bioorganic & Medicinal Chemistry Letters (2021). (Books and Publications: Article (Peer-reviewed)) 2021
Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, and Emilio Gallicchio. Alchemical Transformations for Concerted Hydration Free Energy Estimation with Explicit Solvation. J. Chem. Phys. 154, 054103 (2021) (Books and Publications: Article (Peer-reviewed)) 2021
Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, and Emilio Gallicchio. Application of the Alchemical Transfer and Potential of Mean Force Methods to the SAMPL8 Host-Guest Blinded Challenge. ArXiv Preprint 2107.05155 (2021). (Books and Publications: Article (Other)) 2021
Celine Tse, Lauren Wickstrom, Mamuka Kvaratskhelia, Emilio Gallicchio, Ronald Levy, Nanjie Deng. Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor. Biophysical Journal, 119, 1226-1238 (2020). (Books and Publications: Article (Peer-reviewed)) 2020
Ellen Bak, Jennifer T. Miller, Andrea Noronha, John Tavis, Emilio Gallicchio, Ryan P. Murelli and Stuart F.J. Le Grice. 3,7-Dihydroxytropolones Inhibit Initiation of Hepatitis B Virus Minus-Strand DNA Synthesis. Molecules 25, 4434 (2020). (Books and Publications: Article (Peer-reviewed)) 2020
Jeffrey Cruz, Lauren Wickstrom, Danzhou Yang, Emilio Gallicchio, Nanjie Deng. Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. J. of Chemical Theory and Computation (2020). https://doi.org/10.1021/acs.jctc.9b01119 (Books and Publications: Article (Peer-reviewed)) 2020
Qilan Li, Elena Lomonosova, Maureen J. Donlin, Feng Cao, Austin O'Dea, Brienna Milleson, Alex J. Berkowitz, John-Charles Baucom, John P. Stasiak, Daniel V. Schiavone, Rudolf G. Abdelmessih, Anastasiya Lyubimova, Americo J. Fraboni, Lauren P. Bejcek, Juan A. Villa, Emilio Gallicchio, Ryan P. Murelli, and John E. Tavis. Amide-containing α-hydroxytropolones as inhibitors of hepatitis B virus replication. Antiviral Research (2020). https://doi.org/10.1016/j.antiviral.2020.104777 (Books and Publications: Article (Peer-reviewed)) 2020
Arghya Chakravorty, Emilio Gallicchio, Emil Alexov. A grid-based algorithm in conjunction with a Gaussian-based model of atoms for describing molecular geometry J. Comp. Chem. Early View (2019). (Books and Publications: Article (Peer-reviewed)) 2019
Junchao Xia, William Flynn, William, Emilio Gallicchio, Keith Uplinger, Jonathan Armstrong, Stefano Forli, Arthur Olson, Ronald Levy. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. J. Chemical Information and Modeling. Just Accepted Manuscript (2019) (Books and Publications: Article (Peer-reviewed)) 2019
Peng He. Sheila Sarkar, Emilio Gallicchio, Tom Kurtzman, and Lauren Wickstrom. The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin. J. of Phys. Chem. B. Just Accepted (2019) (Books and Publications: Article (Peer-reviewed)) 2019
Rajat K. Pal and Emilio Gallicchio. Perturbation Potentials to Overcome Order/Disorder Transitions in Alchemical Binding Free Energy Calculations. J. of Chem. Phys.. 151, 124116 (2019). Featured Article. (Books and Publications: Article (Peer-reviewed)) 2019
Rajat Kumar Pal, Steve Ramsey, Satishkumar Gadhiya, Pierpaolo Cordone, Lauren Wickstrom, Wayne W Harding, Tom Kurtzman, Emilio Gallicchio. Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes. PLoS ONE 14(9): e0222902 (2019). (Books and Publications: Article (Peer-reviewed)) 2019
Xiang Gao, Emilio Gallicchio, and Adrian E. Roitberg. The generalized Boltzmann distribution is the only distribution in which the Gibbs-Shannon entropy equals the thermodynamic entropy. J. Chem. Phys. 151, 034113 (2019) (Books and Publications: Article (Peer-reviewed)) 2019
Denise Kilburg and Emilio Gallicchio. Analytical Model of the Free Energy of Alchemical Molecular Binding. J. Chem. Theory Comput. 14, 6183-6196 (2018). (Books and Publications: Article (Peer-reviewed)) 2018
Denise Kilburg and Emilio Gallicchio. Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes. Frontiers Molecular Biosciences: Molecular Recognition (2018). doi:10.3389/fmolb.2018.00022 (Books and Publications: Article (Peer-reviewed)) 2018
Satishkumar Gadhiya, Pierpaolo Cordone, Rajat K. Pal, Emilio Gallicchio, Lauren Wickstrom, Tom Kurtzman, Steven Ramsey, and Wayne W. Harding. 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 (2018). (Books and Publications: Article (Peer-reviewed)) 2018
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). (Books and Publications: Article (Peer-reviewed)) 2017
D. R. Hirsch, D. V. Schiavone, A. J. Berkowitz, L. A. Morrison, T. Masaoka, J. A. Wilson, E. Lomonosova, H. Zhao, B. S. Patel, S. H. Datla, S. G. Hoft, S. J. Majidi, R. K. Pal, E. Gallicchio, L. Tang, J. E. Tavis, S. F. J. Le Grice, J. A. Beutler and R. P. Murelli. Synthesis and biological assessment of 3,7-dihydroxytropolones. Organic & Biomolecular Chemistry (2017). doi:10.1039/C7OB02453C (Books and Publications: Article (Peer-reviewed)) 2017
Emilio Gallicchio. Alchemical Response Parameters from an Analytical Model of Molecular Binding (2017). arXiv:1707.00769 (Books and Publications: Article (Other)) 2017
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) (Books and Publications: Article (Peer-reviewed)) 2016
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) (Books and Publications: Article (Peer-reviewed)) 2016
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). (Books and Publications: Book Chapter) 2016
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. (Books and Publications: Article (Peer-reviewed)) 2016
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. J. Comp. Aided. Mol. Des. (2016) (Books and Publications: Article (Peer-reviewed)) 2016
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. 2016. *Undergraduate student. (Books and Publications: Article (Peer-reviewed)) 2016
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) (Books and Publications: Article (Peer-reviewed)) 2016
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. (Books and Publications: Article (Peer-reviewed)) 2015
Deng, Nan-jie, Stefano Forli, Peng He, Alex Perryman, Lauren Wickstrom, Suyambu Kesava Vijayan, Theresa Tiefenbrunn, C. Stout, Emilio Gallicchio, Arthur Olson and Ronald M. Levy. "Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease." Journal of Physical Chemistry B 119: 976-88. (Books and Publications: Article (Peer-reviewed)) 2015
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. (Books and Publications: Article (Peer-reviewed)) 2015
Gallicchio, Emilio, 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." Journal of Computer-Aided Molecular Design 29: 315-25. (Books and Publications: Article (Peer-reviewed)) 2015
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. (Books and Publications: Article (Peer-reviewed)) 2015
Gallicchio, Emilio, 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." Journal of Computer-Aided Molecular Design 28: 475-90. (Books and Publications: Article (Peer-reviewed)) 2014
Radak, Brian K., Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy and 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. (Books and Publications: Article (Peer-reviewed)) 2013
Wickstrom, L., P. He, E. Gallicchio and R.M. Levy. "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: 3136-50. (Books and Publications: Article (Peer-reviewed)) 2013
Yi, Guohua, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold and Gail Ferstandig Arnold. "Chmeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses." PLoS ONE 8.9: e72205. (Books and Publications: Article (Peer-reviewed)) 2013
"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. (Books and Publications: Article (Peer-reviewed)) 2012
Bell, J.A., Y. Cao, J.R. Gunn, T. Day, E. Gallicchio, Z. Zhou, R.M. Levy and R. Farid. "PrimeX and the Schrödinger Computational Chemistry Suite of Programs." International Tables for Crystallography: 534-38. (Books and Publications: Article (Peer-reviewed)) 2012
Gallicchio, E. and R.M. Levy. "Prediction of SAMPL3 Host-Guest Affinities With the Binding Energy Distribution Analysis Method (BEDAM)." Journal of Computer-Aided Molecular Design 26: 505-16. (Books and Publications: Article (Peer-reviewed)) 2012
Lapelosa, M., E. Gallicchio and R.M. Levy. "Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations." Journal of Chemical Theory and Computation 8: 44-60. JCTC Most Read Article, Q1 2012. (Books and Publications: Article (Peer-reviewed)) 2012
Tan, Z., E. Gallicchio, M. Lapelosa and R.M. Levy. "Theory of Binless Multi-state Free Energy Estimation With Applications to Protein-ligand Binding." Journal of Chemical Physics 136: 144102. (Books and Publications: Article (Peer-reviewed)) 2012
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." Journal of the American Chemical Society 133: 9387-94. (Books and Publications: Article (Peer-reviewed)) 2011
Gallicchio, E. and R.M. Levy. "Advances in All Atom Sampling Methods for Modeling Protein-ligand Binding Affinities." Current Opinions in Structural Biology 21: 161-66. (Books and Publications: Article (Peer-reviewed)) 2011
Gallicchio, Emilio 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. (Books and Publications: Article (Peer-reviewed)) 2011
Wickstrom, L., E. Gallicchio and R.M. Levy. "The Linear Interaction Energy Method for the Prediction of Stability Changes Upon Mutation." Proteins 80: 111-25. (Books and Publications: Article (Peer-reviewed)) 2011
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." Journal of Physical Chemistry B 115: 1512-23. (Books and Publications: Article (Peer-reviewed)) 2011
Gallicchio, E., M. Lapelosa and R.M. Levy. "Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-ligand Binding Affinities." Journal of Chemical Theory and Computation 6: 2961-77. (Books and Publications: Article (Peer-reviewed)) 2010
Lapelosa, M., Arnold G. Ferstandig, E. Gallicchio, E. Arnold and R.M. Levy. "Antigenic Characteristics of Rhinovirus Chimeras Designed in Silico for Enhanced Presentation of HIV-1 gp41 Epitopes." Journal of Molecular Biology 397: 752-66. (Books and Publications: Article (Peer-reviewed)) 2010
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 (Books and Publications: Article (Peer-reviewed)) 2009
Gallicchio, E., K. Paris and R.M. Levy. "The AGBNP2 Implicit Solvent Model." Journal of Chemical Theory and Computation 5: 2544-64. (Books and Publications: Article (Peer-reviewed)) 2009
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 (Books and Publications: Article (Peer-reviewed)) 2009
Okumura, H., E. Gallicchio and R.M. Levy. "Conformational Populations of Ligand-sized Molecules by Replica Exchange Molecular Dynamics and Temperature Reweighting." Journal of Computational Chemistry 31: 1357-67. (Books and Publications: Article (Peer-reviewed)) 2009
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 (Books and Publications: Article (Peer-reviewed)) 2009
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 (Books and Publications: Article (Peer-reviewed)) 2008
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). (Books and Publications: Book Chapter) 2008
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 (Books and Publications: Article (Peer-reviewed)) 2008
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 (Books and Publications: Article (Peer-reviewed)) 2008
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+ (Books and Publications: Article (Peer-reviewed)) 2008
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 (Books and Publications: Article (Peer-reviewed)) 2007
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 (Books and Publications: Article (Peer-reviewed)) 2007
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 (Books and Publications: Article (Peer-reviewed)) 2007
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 (Books and Publications: Article (Peer-reviewed)) 2006
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 (Books and Publications: Article (Peer-reviewed)) 2006
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 (Books and Publications: Article (Peer-reviewed)) 2005
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 (Books and Publications: Article (Peer-reviewed)) 2005
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 (Books and Publications: Article (Peer-reviewed)) 2005
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 (Books and Publications: Article (Peer-reviewed)) 2005
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 (Books and Publications: Article (Peer-reviewed)) 2004
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 (Books and Publications: Article (Peer-reviewed)) 2004
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 (Books and Publications: Article (Peer-reviewed)) 2004
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). (Books and Publications: Article (Peer-reviewed)) 2003
Chernyavsky, B., E. Gallicchio, D. Knight, R. Levy, and A. Page. The Rutgers Computational Grid: A Distributed Linux PC Cluster. Cluster Computing (2002) (Books and Publications: Article (Peer-reviewed)) 2002
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). (Books and Publications: Article (Peer-reviewed)) 2002
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. (Books and Publications: Article (Peer-reviewed)) 2002
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). (Books and Publications: Article (Peer-reviewed)) 2002
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). (Books and Publications: Article (Peer-reviewed)) 2002
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). (Books and Publications: Article (Peer-reviewed)) 2001
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). (Books and Publications: Article (Peer-reviewed)) 2001
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). (Books and Publications: Article (Peer-reviewed)) 2000
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). (Books and Publications: Article (Peer-reviewed)) 1999
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). (Books and Publications: Article (Peer-reviewed)) 1998
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). (Books and Publications: Article (Peer-reviewed)) 1998
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). (Books and Publications: Article (Peer-reviewed)) 1998
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). (Books and Publications: Article (Peer-reviewed)) 1998
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). (Books and Publications: Article (Peer-reviewed)) 1997
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). (Books and Publications: Article (Peer-reviewed)) 1997
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). (Books and Publications: Article (Peer-reviewed)) 1996
F. Battaglia, T.F. George, E. Gallicchio. " Lezioni di Fisica Classica e Quantistica " , CEDAM, Padova, Italy, 1996. (Books and Publications: Book (Authored)) 1996
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). (Books and Publications: Article (Peer-reviewed)) 1994
E. Gallicchio, F. Battaglia.FORTRAN Routine to Compute Born-Oppenheimer Potential Energy Curves Directly from Spectroscopic Data, J. Comput. Chem., 14, 579 (1993) (Books and Publications: Article (Peer-reviewed)) 1993
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). (Books and Publications: Article (Peer-reviewed)) 1993
Awards, Honors and Fellowships
Levy-Kosminsky Professorship in Physical Chemistry (Awards and Honors) 2023
NIH/NIGMS AREA R15 Research Grant R15GM151708-01: "Enhancing Drug Discovery Research by Free Energy Modeling" $463,020 9/25/2023-8/31/2026 (Grants and Fellowships) 2023
Leadership Resource Allocation (LRAC) Award MCB20003, Frontera GPU: 5,950.0 Node Hours to perform a "Large-Scale Computational Screening on Leadership Resources to Assess the Estrogenic Potential of Environmental Chemicals" (Grants and Fellowships) 2020
OpenEye American Chemical Society COMP Outstanding Junior Faculty Award (Awards and Honors) 2020
Levy-Kosminsky Professorship in Physical Chemistry (Awards and Honors) 2018
NSF CAREER, "Theory, Models and Computer Simulation of Molecular Recognition Processes", $631,358.00, September 2018 to August 2023 (Grants and Fellowships) 2018
Henry Wasser Award. This award is given to outstanding CUNY Assistant Professors by the CUNY Academy for the Humanities and Sciences. (Awards and Honors) 2017
NVIDIA GPU Best Poster Award at the 254th ACS National Meeting & Exposition in Washington DV for "Efficient GPU/OpenMM implementation of the AGBNP solvation model for macromolecular binding"
(Awards and Honors) 2017
CUNY CIRG "A Combined Treatment of Hydration and Dynamical Effects for the Modeling of Protein-Ligand Binding Thermodynamics" 2016-2017. $40,000 (Grants and Fellowships) 2016
NSF "SI2-SSE: High-Performance Software for Large-Scale Modeling of Binding Equilibria", 2014-2016. $142,000 (Grants and Fellowships) 2014
