Emilio Gallicchio

发表

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

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

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..

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

R. Levy, E. Gallicchio, Emilio Gallicchio, 1998, Annual review of physical chemistry.

The generalized Boltzmann distribution is the only distribution in which the Gibbs-Shannon entropy equals the thermodynamic entropy.

E. Gallicchio, A. Roitberg, Xiang Gao, 2019, The Journal of chemical physics.

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

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

A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors

E. Gallicchio, C. Bagni, I. d'Annessa, 2015, Protein science : a publication of the Protein Society.

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..

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

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

Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited

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

The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.

L. Wickstrom, Peng He, Sheila Sarkar, 2019, The journal of physical chemistry. B.

Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes

Satishkumar V. Gadhiya, E. Gallicchio, W. Harding, 2019, PloS one.

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.

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.

Theory of binless multi-state free energy estimation with applications to protein-ligand binding.

Z. Tan, R. Levy, E. Gallicchio, 2012, The Journal of chemical physics.

On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models

R. Levy, E. Gallicchio, N. Matubayasi, 1998 .

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.

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..

Amide-containing α-hydroxytropolones as inhibitors of hepatitis B virus replication.

E. Gallicchio, J. Tavis, M. Donlin, 2020, Antiviral research.

What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling

Sheenam Khuttan, Emilio Gallicchio, 2023, 2310.14350.

Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands

W. Sherman, Huafeng Xu, Chuanjie Wu, 2023, J. Chem. Inf. Model..

Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host-guest SAMPL9 blinded challenge.

E. Gallicchio, Huafeng Xu, Chuanjie Wu, 2023, Physical chemistry chemical physics : PCCP.

Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series

E. Gallicchio, G. D. Fabritiis, Francesc Sabanés Zariquiey, 2023, J. Chem. Inf. Model..

Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method

E. Gallicchio, S. Azimi, Sheenam Khuttan, 2021, J. Chem. Inf. Model..

Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge

N. Deng, S. Azimi, T. Kurtzman, 2021, Journal of Computer-Aided Molecular Design.

Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations.

E. Gallicchio, R. Pal, Emilio Gallicchio, 2019, The Journal of chemical physics.

Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.

E. Gallicchio, G. D. Fabritiis, Francesc Sabanés Zariquiey, 2023, ArXiv.

Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.

E. Gallicchio, N. Deng, S. Azimi, 2021, Journal of chemical theory and computation.

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.

R. Levy, E. Gallicchio, L. Wickstrom, 2020, Biophysical journal.

Alchemical transformations for concerted hydration free energy estimation with explicit solvation.

S. Azimi, Sheenam Khuttan, Joe Z. Wu, 2020, The Journal of chemical physics.

Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.

E. Gallicchio, Danzhou Yang, L. Wickstrom, 2020, Journal of chemical theory and computation.

Asynchronous replica exchange software for grid and heterogeneous computing

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

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.

Parameterization of an effective potential for protein–ligand binding from host–guest affinity data

M. Gilson, R. Levy, E. Gallicchio, 2016, Journal of molecular recognition : JMR.

Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.

R. Levy, E. Gallicchio, L. Wickstrom, 2013, Journal of chemical theory and computation.

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.

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..

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

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

Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected].

R. Levy, E. Gallicchio, E. Arnold, 2010, Journal of molecular biology.

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.

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.

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.

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.

Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.

E. Gallicchio, L. Wickstrom, Lieyang Chen, 2022, Physical chemistry chemical physics : PCCP.

The Rutgers Computational Grid: A Distributed Linux PC Cluster

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

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..

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.

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

Anthony K. Felts, R. Levy, A. K. Felts, 2002, Proteins.

Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Anthony K. Felts, R. Levy, A. K. Felts, 2002 .

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

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

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.

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

Peng He, Zhiqiang Tan, Ronald M. Levy, 2015, 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..

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

R. Levy, A. Olson, W. Flynn, 2019, J. Chem. Inf. Model..

Analytical Model of the Free Energy of Alchemical Molecular Binding.

E. Gallicchio, D. Kilburg, Emilio Gallicchio, 2018, Journal of chemical theory and computation.

Alchemical Response Parameters from an Analytical Model of Molecular Binding

E. Gallicchio, Emilio Gallicchio, 2017, 1707.00769.

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..

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.

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.

Simulating replica exchange simulations of protein folding with a kinetic network model

R. Levy, M. Andrec, E. Gallicchio, 2007, Proceedings of the National Academy of Sciences.

Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes

E. Gallicchio, D. Kilburg, Emilio Gallicchio, 2018, Front. Mol. Biosci..

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.

The AGBNP2 Implicit Solvation Model.

R. Levy, E. Gallicchio, K. Paris, 2009, Journal of chemical theory and computation.

Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En 5 hanced Presentation of HIV-1 gp 41 Epitopes

R. Levy, E. Gallicchio, E. Arnold, 2010 .

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 .

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.

The linear interaction energy method for the prediction of protein stability changes upon mutation

R. Levy, E. Gallicchio, L. Wickstrom, 2012, Proteins.

Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses

R. Levy, E. Gallicchio, E. Arnold, 2013, PloS one.

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

R. Levy, E. Arnold, G. F. Arnold, 2009, Journal of molecular biology.

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.

Anthony K. Felts, R. Levy, A. K. Felts, 2004, Proteins.

Alchemical Transformations for Single-Step Hydration Free Energy Calculations

Emilio Gallicchio, 2020, 2005.06504.

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

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

Free Energy Surfaces of -Hairpin and -Helical Peptides Generated by Replica Exchange Molecular Dynamics with the AGBNP Implicit Solvent Model

Anthony K. Felts, R. Levy, A. K. Felts, 2004 .

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.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.

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

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.

3,7-Dihydroxytropolones Inhibit Initiation of Hepatitis B Virus Minus-Strand DNA Synthesis

E. Gallicchio, J. Tavis, S. L. Le Grice, 2020, Molecules.