Emilio Gallicchio

发表

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

Ronald M. Levy, Emilio Gallicchio, Linda Yu Zhang, 2002, J. Comput. Chem..

Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications

Li Zhang, Manish Parashar, Ronald M. Levy, 2006, 2006 International Conference on Parallel Processing (ICPP'06).

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Zhiqiang Tan, Peng He, Emilio Gallicchio, 2016, The journal of physical chemistry. B.

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

Richard A. Friesner, Anthony K. Felts, Ronald M. Levy, 2005, J. Comput. Chem..

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

Richard A Friesner, Anthony K. Felts, Emilio Gallicchio, 2008, Journal of chemical theory and computation.

AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling

Ronald M. Levy, Emilio Gallicchio, R. Levy, 2004, J. Comput. Chem..

FORTRAN routine to compute Born–Oppenheimer potential energy curves directly from spectroscopic data

Emilio Gallicchio, Franco Battaglia, F. Battaglia, 1993, J. Comput. Chem..

A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry

Emil Alexov, Arghya Chakravorty, Emilio Gallicchio, 2019, J. Comput. Chem..

Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting

Ronald M. Levy, Emilio Gallicchio, Hisashi Okumura, 2009, J. Comput. Chem..

A framework for flexible and scalable replica-exchange on production distributed CI

Wei Dai, Shantenu Jha, Melissa Romanus, 2013, XSEDE.

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

Arthur J. Olson, Lauren Wickstrom, Alex L. Perryman, 2014, Journal of Computer-Aided Molecular Design.

Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models

Anthony K. Felts, Ronald M. Levy, Michael Andrec, 2009 .

Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis

Peng He, Zhiqiang Tan, Ronald M. Levy, 2015, J. Comput. Chem..

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

Baofeng Zhang, Peng He, Ronald M. Levy, 2016, Journal of Computer-Aided Molecular Design.

The Rutgers Computational Grid: A Distributed Linux PC Cluster

Ronald M. Levy, Doyle D. Knight, Emilio Gallicchio, 2003, Cluster Computing.

Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

Lauren Wickstrom, Ronald M. Levy, Emilio Gallicchio, 2016, Journal of Computer-Aided Molecular Design.

Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

Richard A. Friesner, Ronald M. Levy, Emilio Gallicchio, 2001, J. Comput. Chem..

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

Ronald M. Levy, Emilio Gallicchio, R. Levy, 2012, Journal of Computer-Aided Molecular Design.

The Rutgers Computational Grid Based on Linux PC Cluster

Ronald M. Levy, Doyle D. Knight, Emilio Gallicchio, 2001, PPSC.

Asynchronous replica exchange for molecular simulations

Manish Parashar, Ronald M. Levy, Emilio Gallicchio, 2008, J. Comput. Chem..

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units

Vijay S. Pande, Baofeng Zhang, Emilio Gallicchio, 2017, J. Comput. Chem..

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network

Stefano Forli, Emilio Gallicchio, Junchao Xia, 2019, J. Chem. Inf. Model..

Asynchronous replica exchange software for grid and heterogeneous computing

Baofeng Zhang, Ronald M. Levy, Emilio Gallicchio, 2015, Comput. Phys. Commun..

PrimeX and the Schrödinger computational chemistry suite of programs

Ronald M. Levy, Zhiyong Zhou, Emilio Gallicchio, 2012 .

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge

Jie Zhu, He Chen, Yang Gao, 2015, Journal of Computer-Aided Molecular Design.

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

Lauren Wickstrom, Rajat Kumar Pal, Ronald M. Levy, 2016, Journal of Computer-Aided Molecular Design.

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions.

Emilio Gallicchio, Yang Su, Emilio Gallicchio, 2004, Biophysical chemistry.

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Michael Andrec, Emilio Gallicchio, Ronald M Levy, 2011, The journal of physical chemistry. B.

Temperature weighted histogram analysis method, replica exchange, and transition paths.

Anthony K. Felts, Michael Andrec, Emilio Gallicchio, 2005, The journal of physical chemistry. B.

The AGBNP2 Implicit Solvation Model.

Emilio Gallicchio, Ronald M Levy, Kristina Paris, 2009, Journal of chemical theory and computation.

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

Michael Andrec, Emilio Gallicchio, Ronald M Levy, 2009, The journal of physical chemistry. B.

Advances in all atom sampling methods for modeling protein-ligand binding affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2011, Current opinion in structural biology.

Recent theoretical and computational advances for modeling protein-ligand binding affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2011, Advances in protein chemistry and structural biology.

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

Emilio Gallicchio, Ronald M Levy, Anthony K Felts, 2003, Journal of the American Chemical Society.

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2005, Journal of molecular biology.

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study.

Emilio Gallicchio, R. Friesner, R. Levy, 2006, Journal of the American Chemical Society.

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2010, Journal of chemical theory and computation.

On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data

Emilio Gallicchio, Bruce J. Berne, B. Berne, 1996 .

Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.

Emilio Gallicchio, Emilio Gallicchio, 2012, Computational molecular bioscience.

Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability.

Emilio Gallicchio, Ronald M Levy, Eddy Arnold, 2009, Journal of medicinal chemistry.

On the application of numerical analytic continuation methods to the study of quantum mechanical vibrational relaxation processes

Emilio Gallicchio, Bruce J. Berne, S. A. Egorov, 1998 .

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.

Richard A Friesner, Jennifer L. Knight, Emilio Gallicchio, 2008, Acta crystallographica. Section D, Biological crystallography.

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

Emilio Gallicchio, Bruce J. Berne, B. Berne, 1994 .

In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes.

Emilio Gallicchio, Ronald M Levy, Eddy Arnold, 2009, Journal of molecular biology.

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

Arthur J. Olson, Lauren Wickstrom, Stefano Forli, 2014, The journal of physical chemistry. B.

Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited

Ronald M. Levy, Emilio Gallicchio, R. Levy, 1998 .

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

Emilio Gallicchio, Ronald M Levy, Eddy Arnold, 2007, Journal of chemical theory and computation.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2012, Journal of chemical theory and computation.