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ORCIDEmilio Gallicchio
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2020 – today
- 2024
[j24]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)- [j23]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) - 2023
- [j22]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) - [i1]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:
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. CoRR abs/2310.03121 (2023) - 2022
- [j21]Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, Emilio Gallicchio:
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge. J. Comput. Aided Mol. Des. 36(1): 63-76 (2022) - [j20]Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat Kumar Pal, Emilio Gallicchio:
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. J. Chem. Inf. Model. 62(2): 309-323 (2022)
2010 – 2019
- 2019
- [j19]Arghya Chakravorty, Emilio Gallicchio, Emil Alexov:
A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J. Comput. Chem. 40(12): 1290-1304 (2019) - [j18]Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
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. 59(4): 1382-1397 (2019) - 2017
- [j17]Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. 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. Comput. Aided Mol. Des. 31(1): 29-44 (2017) - [j16]Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio:
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. 31(1): 45 (2017) - [j15]Baofeng Zhang, Denise Kilburg, Peter K. Eastman, Vijay S. Pande, Emilio Gallicchio:
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. J. Comput. Chem. 38(10): 740-752 (2017) - 2016
- [j14]Nan-Jie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy:
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. 30(9): 743-751 (2016) - 2015
- [j13]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. Comput. Phys. Commun. 196: 236-246 (2015) - [j12]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:
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J. Comput. Aided Mol. Des. 29(4): 315-325 (2015) - [j11]Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy:
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J. Comput. Chem. 36(23): 1772-1785 (2015) - 2014
- [j10]Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28(4): 475-490 (2014) - 2013
- [c4]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. XSEDE 2013: 26:1-26:8 - 2012
- [j9]Emilio Gallicchio, Ronald M. Levy:
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J. Comput. Aided Mol. Des. 26(5): 505-516 (2012) - [c3]Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallicchio, André Merzky, Yaakoub El Khamra, Shantenu Jha:
The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE. XSEDE 2012: 46:1-46:9 - 2010
- [j8]Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy:
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J. Comput. Chem. 31(7): 1357-1367 (2010)
2000 – 2009
- 2008
- [j7]Emilio Gallicchio, Ronald M. Levy, Manish Parashar:
Asynchronous replica exchange for molecular simulations. J. Comput. Chem. 29(5): 788-794 (2008) - 2006
- [c2]Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy:
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. ICPP 2006: 127-134 - 2005
- [j6]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:
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comput. Chem. 26(16): 1752-1780 (2005) - 2004
- [j5]Emilio Gallicchio, Ronald M. Levy:
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. 25(4): 479-499 (2004) - 2003
- [j4]Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy, Andy Page:
The Rutgers Computational Grid: A Distributed Linux PC Cluster. Clust. Comput. 6(3): 267-278 (2003) - 2002
- [j3]Emilio Gallicchio, Linda Yu Zhang, Ronald M. Levy:
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. 23(5): 517-529 (2002) - 2001
- [j2]Linda Yu Zhang, Emilio Gallicchio, Richard A. Friesner, Ronald M. Levy:
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. J. Comput. Chem. 22(6): 591-607 (2001) - [c1]Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy:
The Rutgers Computational Grid Based on Linux PC Cluster. PP 2001
1990 – 1999
- 1993
- [j1]Franco Battaglia, Emilio Gallicchio:
FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data. J. Comput. Chem. 14(5): 579-586 (1993)
Coauthor Index
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