Emilio Gallicchio

30 papers B 1Journal 26Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.
J. Chem. Inf. Model.
Emilio Gallicchio
2024 J jnl
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials.
J. Chem. Inf. Model.
Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis
2024 J jnl
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands.
J. Chem. Inf. Model.
Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio
2023 J jnl
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
CoRR
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, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João P. G. L. M. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland
2023 J jnl
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.
J. Chem. Inf. Model.
Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis
2022 J jnl
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.
J. Comput. Aided Mol. Des.
Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, Emilio Gallicchio
2022 J jnl
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method.
J. Chem. Inf. Model.
Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat Kumar Pal, Emilio Gallicchio
2019 J jnl
A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.
J. Comput. Chem.
Arghya Chakravorty, Emilio Gallicchio, Emil Alexov
2019 J jnl
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.
J. Chem. Inf. Model.
Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2017 J jnl
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
J. Comput. Aided Mol. Des.
Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
2017 J jnl
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.
J. Comput. Chem.
Baofeng Zhang, Denise Kilburg, Peter K. Eastman, Vijay S. Pande, Emilio Gallicchio
2017 J jnl
Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
J. Comput. Aided Mol. Des.
Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
2016 J jnl
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
J. Comput. Aided Mol. Des.
Nan-Jie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy
2015 J jnl
Asynchronous replica exchange software for grid and heterogeneous computing.
Comput. Phys. Commun.
Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy
2015 J jnl
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.
J. Comput. Aided Mol. Des.
Emilio Gallicchio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi A. Pethe, Jie Zhu, Ronald M. Levy
2015 J jnl
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.
J. Comput. Chem.
Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy
2014 J jnl
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.
J. Comput. Aided Mol. Des.
Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2013 — conf
A framework for flexible and scalable replica-exchange on production distributed CI.
XSEDE
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
2012 J jnl
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).
J. Comput. Aided Mol. Des.
Emilio Gallicchio, Ronald M. Levy
2012 — conf
The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE.
XSEDE
Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallicchio, André Merzky, Yaakoub El Khamra, Shantenu Jha
2010 J jnl
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.
J. Comput. Chem.
Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy
2008 J jnl
Asynchronous replica exchange for molecular simulations.
J. Comput. Chem.
Emilio Gallicchio, Ronald M. Levy, Manish Parashar
2006 B conf
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications.
ICPP
Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy
2005 J jnl
Integrated Modeling Program, Applied Chemical Theory (IMPACT).
J. Comput. Chem.
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, Matthew P. Repasky, Linda Yu Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy
2004 J jnl
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
J. Comput. Chem.
Emilio Gallicchio, Ronald M. Levy
2003 J jnl
The Rutgers Computational Grid: A Distributed Linux PC Cluster.
Clust. Comput.
Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy, Andy Page
2002 J jnl
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.
J. Comput. Chem.
Emilio Gallicchio, Linda Yu Zhang, Ronald M. Levy
2001 J jnl
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations.
J. Comput. Chem.
Linda Yu Zhang, Emilio Gallicchio, Richard A. Friesner, Ronald M. Levy
2001 — conf
The Rutgers Computational Grid Based on Linux PC Cluster.
PP
Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy
1993 J jnl
FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data.
J. Comput. Chem.
Franco Battaglia, Emilio Gallicchio