FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data. - Franco Battaglia; Emilio Gallicchio (J. Comput. Chem., 1993)

The Rutgers Computational Grid Based on Linux PC Cluster. - Boris M. Chernyavsky; Emilio Gallicchio; Doyle D. Knight; Ronald M. Levy (PP, 2001)

Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. - Linda Yu Zhang; Emilio Gallicchio; Richard A. Friesner; Ronald M. Levy (J. Comput. Chem., 2001)

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. - Emilio Gallicchio; Linda Yu Zhang; Ronald M. Levy (J. Comput. Chem., 2002)

The Rutgers Computational Grid: A Distributed Linux PC Cluster. - Boris M. Chernyavsky; Emilio Gallicchio; Doyle D. Knight; Ronald M. Levy; Andy Page (Clust. Comput., 2003)

AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. - Emilio Gallicchio; Ronald M. Levy (J. Comput. Chem., 2004)

Integrated Modeling Program, Applied Chemical Theory (IMPACT). - Jay L. Banks; Hege S. Beard; Yixiang X. Cao; Art E. Cho; Wolfgang Damm; Ramy Farid; Anthony K. Felts; Thomas A. Halgren; Daniel T. Mainz; Jon R. Maple; Robert B. Murphy; Dean M. Philipp; et al. (J. Comput. Chem., 2005)

Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. - Li Zhang; Manish Parashar; Emilio Gallicchio; Ronald M. Levy (ICPP, 2006)

Asynchronous replica exchange for molecular simulations. - Emilio Gallicchio; Ronald M. Levy; Manish Parashar (J. Comput. Chem., 2008)

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. - Hisashi Okumura; Emilio Gallicchio; Ronald M. Levy (J. Comput. Chem., 2010)

The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE. - Melissa Romanus; Pradeep Kumar Mantha; Matt McKenzie; Thomas C. Bishop; Emilio Gallicchio; André Merzky; Yaakoub El Khamra; Shantenu Jha (XSEDE, 2012)

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). - Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2012)

A framework for flexible and scalable replica-exchange on production distributed CI. - 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 (XSEDE, 2013)

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. - Emilio Gallicchio; Nan-Jie Deng; Peng He; Lauren Wickstrom; Alexander L. Perryman; Daniel N. Santiago; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Comput. Aided Mol. Des., 2014)

Asynchronous replica exchange software for grid and heterogeneous computing. - Emilio Gallicchio; Junchao Xia; William F. Flynn; Baofeng Zhang; Sade Samlalsingh; Ahmet Mentes; Ronald M. Levy (Comput. Phys. Commun., 2015)

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. - Emilio Gallicchio; Haoyuan Chen; He Chen; Michael Fitzgerald; Yang Gao 019; Peng He; Malathi Kalyanikar; Chuan Kao; Beidi Lu; Yijie Niu; Manasi A. Pethe; Jie Zhu; et al. (J. Comput. Aided Mol. Des., 2015)

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Bin W. Zhang; Peng He; Zhiqiang Tan; Ronald M. Levy (J. Comput. Chem., 2015)

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. - Nan-Jie Deng; William F. Flynn; Junchao Xia; R. S. K. Vijayan; Baofeng Zhang; Peng He; Ahmet Mentes; Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2016)

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2017)

Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2017)

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. - Baofeng Zhang; Denise Kilburg; Peter K. Eastman; Vijay S. Pande; Emilio Gallicchio (J. Comput. Chem., 2017)

A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. - Arghya Chakravorty; Emilio Gallicchio; Emil Alexov (J. Comput. Chem., 2019)

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Keith Uplinger; Jonathan D. Armstrong; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Chem. Inf. Model., 2019)

Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge. - Solmaz Azimi; Joe Z. Wu; Sheenam Khuttan; Tom Kurtzman; Nanjie Deng; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2022)

Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. - Solmaz Azimi; Sheenam Khuttan; Joe Z. Wu; Rajat Kumar Pal; Emilio Gallicchio (J. Chem. Inf. Model., 2022)

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. - Peter K. Eastman; Raimondas Galvelis; Raúl P. Peláez; Charlles R. A. Abreu; Stephen E. Farr; Emilio Gallicchio; Anton Gorenko; Michael M. Henry; Frank Hu; Jing Huang 004; Andreas Krämer; Julien Michel; et al. (CoRR, 2023)

Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series. - Francesc Sabanés Zariquiey; Adrià Pérez; Maciej Majewski; Emilio Gallicchio; Gianni De Fabritiis (J. Chem. Inf. Model., 2023)

Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. - Lieyang Chen; Yujie Wu; Chuanjie Wu; Ana Silveira; Woody Sherman; Huafeng Xu; Emilio Gallicchio (J. Chem. Inf. Model., 2024)

Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. - Francesc Sabanés Zariquiey; Raimondas Galvelis; Emilio Gallicchio; John D. Chodera; Thomas E. Markland; Gianni De Fabritiis (J. Chem. Inf. Model., 2024)

Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping. - Emilio Gallicchio (J. Chem. Inf. Model., 2025)