Biography


Dr. Emilio Gallicchio
State University of New Jersey, USA


Email: emilio.gallicchio@rutgers.edu


Qualifications


1996 Ph.D., Chemical Physics, Columbia University, USA

1995 M.Phil., Chemical Physics, Columbia University, USA
1992 M.A., Chemical Physics, Columbia University, USA
1991 B.A., University of Basilicata, Italy


Publications(Selected)

  1. Lapelosa M, Gallicchio E and Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J. Chem Theory Comput, in press (2012).
  2. Wickstrom L, Gallicchio E and Levy RM. The Linear Interaction Energy Method for the Prediction of Stability Changes Upon Mutation. Proteins, in press (2011).
  3. Gallicchio E and Levy RM. Recent Theoretical and Computational Advances for Modeling Protein-Ligand Binding Affinities. In Christo Christov, editor: Advances in Protein Chemistry and Structural Biology, 85, 27-80, Academic Press (2011).
  4. 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)
  5. 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).
  6. Gallicchio E, Lapelosa M and Levy RM. The binding energy distribution analysis method (BEDAM) for the estimation of protein-ligand binding affinities. J Chem Theory Comput, 6, 2961-2977 (2010).
  7. 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)
  8. 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)
  9. Gallicchio E, Paris K, and Levy RM. The AGBNP2 Implicit Solvent Model. J Chem Theory Comput, 5, 2544-2564 (2009).
  10. 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).
  11. 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).
  12. Lapelosa M, Gallicchio E, Ferstandig Arnold G, Arnold E, and Levy RM. In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J Mol Biol, 385, 675-691 (2009).
  13. 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).
  14. 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. Comput., 4, 855-858 (2008).
  15. 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).
  16. Gallicchio, E., R.M. Levy, and M. Parashar. Asynchronous Replica Exchange for Molecular Simulations. J. Comp. Chem., 29, 788-794 (2008).
  17. 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).
  18. 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).
  19. 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).
  20. Su Y, Gallicchio E, Das KE, Arnold E and 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, J Chem Theory Comput, 3, 256-277 (2007).
  21. Ravindranathan KP, Gallicchio E, Friesner RA, McDermott AE and Levy RM. 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).
  22. 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.
  23. 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).
  24. 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, Friesner RA, Gallicchio E, and Levy RM. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comp Chem, 26, 1752 (2005).
  25. Andrec, M., A.K. Felts, E. Gallicchio, and R.M. Levy. Protein Folding Pathways from Replica Exchange Simulations and a Kinetic Network Model. Proc. Natl. Acad. Sci. USA, 102, 6801-6806 (2005).
  26. Gallicchio E, Andrec M, Felts AK, and Levy RM. Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths. J Phys Chem B, 109, 6722-6731 (2005).
  27. 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).
  28. Su Y and 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. Biophys. Chem, 109, 251-260 (2004).
  29. Gallicchio E and Levy RM. AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comp Chem, 25, 479-499 (2004).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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.
  36. Chernyavsky, B., E. Gallicchio, D. Knight, R. Levy, and A. Page. The Rutgers Computational Grid: A Distributed Linux PC Cluster. Cluster Computing (2002)
  37. 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)
  38. Gallicchio E, Kubo M and Levy RM. 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).
  39. 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).
  40. 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).
  41. Gallicchio E, Kubo MM and Levy RM. Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited. J Am Chem Soc, 120, 4526-4527 (1998).
  42. 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).
  43. 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).
  44. 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).
  45. 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).
  46. Gallicchio E and Berne BJ. 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).
  47. F. Battaglia, T.F. George, E. Gallicchio. " Lezioni di Fisica Classica e Quantistica " , CEDAM, Padova, Italy, 1996.
  48. 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).
  49. 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).
  50. E. Gallicchio, F. Battaglia.FORTRAN Routine to Compute Born-Oppenheimer Potential Energy Curves Directly from Spectroscopic Data, J. Comput. Chem., 14, 579 (1993).
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