Publications

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• 1. Solmaz Azimi and Emilio Gallicchio. Potential Distribution Theory of Alchemical Transfer. ArXiv:2407.14713 (2024). arXiv 

  2. Solmaz Azimi and Emilio Gallicchio. Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations. ArXiv:2402.06887 (2024). arXiv 

  3. Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D Chodera, Thomas E Markland, Gianni De Fabritiis. Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials. J. Chem. Inf. Model 64, 5, 1481–1485 (2024). doi:10.1021/acs.jcim.3c02031

  4. Lauren Bejcek, Orugbani Eli, Anastasiya Lyubibova , Diana Kapkayeva, Jordan Nafie, John Beutler, Emilio Gallicchio, Dan Sackett, Ryan Murelli.  Studies on a Type III Atropisomeric Colchicine Analog Enabled by an Intermolecular Oxidopyrylium (5 + 2) Cycloaddition/Reductive Ring-Opening Sequence. ChemRxiv:v368j (2023). ChemRxiv

  5. Sheenam Khuttan and Emilio Gallicchio. What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.  J. Chem. Theory Comput. 20, 3, 1489–1501 (2024).  doi:10.1021/acs.jctc.3c01250  arXiv

  6. Peter Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Michael M. Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João PGLM Rodrigues, Jaime Rodriguez-Guerra, Andrew C. Simmonett, Jason Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. J. Phys. Chem. B 128, 1, 109–116 (2024) doi:10.1021/acs.jpcb.3c06662  arXiv

  7. 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. J. Chem. Inf. Model. 64 (1), 250–264 (2024). doi:10.1021/acs.jcim.3c01705 arXiv

  8. 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).  doi:10.1021/acs.jcim.3c00178  arXiv

  9. 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).  doi:10.1039/D3CP02125D arXiv

  10. 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). doi: 10.1039/d1cp05075c 

  11. 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).  doi:10.1021/acs.jcim.1c01129.

  12. 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. J. Comp. Aided. Mol. Des. 36, 63 (2022). doi:10.1007/s10822-021-00437-y. Free copy from the NSF

  13. 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). doi:10.1021/acs.jctc.1c00266 FreeArticle arXiv

  14. 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).

  15. 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). doi:10.1007/978-1-0716-1855-4_15   Free copy from the NSF

  16. 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). doi:10.1063/5.0036944  pdf

  17. 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). link

  18. 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). doi:10.1016/j.bpj.2020.08.005

  19. 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). doi:10.1021/acs.jctc.9b01119

  20. 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) doi:10.1016/j.antiviral.2020.104777

  21. 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. doi:10.1063/1.5123154 Arxiv

  22. 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). doi:10.1371/journal.pone.0222902

  23. 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. 123, 40, 8378-8386 (2019). doi:10.1021/acs.jpcb.9b07028 ChemRxiv 

  24. 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). doi:10.1063/1.5111333 Arxiv

  25. 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, 59, 1382-1397 (2019) doi:10.1021/acs.jcim.8b00817

  26. 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. 40,1290-1304 (2019). doi:10.1002/jcc.25786

  27. Denise Kilburg and Emilio Gallicchio. Analytical Model of the Free Energy of Alchemical Molecular Binding. J. Chem. Theory Comput. 14, 6183–6196 (2018). doi:10.1021/acs.jctc.8b00967 pdf of submitted manuscript

  28. 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). doi:10.1021/acsmedchemlett.8b00229

  29. 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 5, 22 (2018). doi:10.3389/fmolb.2018.00022 pdf of submitted manuscript

  30. 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 16, 62-69 (2018). doi:10.1039/C7OB02453C

  31. 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

  32. 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

  33. 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

  34. 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 

  35. Nanjie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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.

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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).  doi:10.1063/1.3701175

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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).

  67. 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

  68. 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+

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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).

  84. 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).

  85. 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).

  86. 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).

  87. 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).

  88. 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.

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

  90. 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).

  91. 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).

  92. 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).

  93. 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).

  94. 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).

  95. 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).

  96. 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).

  97. 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).

  98. 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).

  99. 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).

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

  101. 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).

  102. 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).

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

  104. 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