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List of works by Emilio Gallicchio

A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties†

scientific article published in July 2001

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

scientific article published on 30 September 2016

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

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

scientific article published on 30 January 2019

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

scientific article

Advances in all atom sampling methods for modeling protein–ligand binding affinities ⬇️

scientific article published on February 19, 2011

Alchemical Transfer Approach to Absolute Binding Free Energy Estimation

scientific article published on 13 May 2021

Analytical Model of the Free Energy of Alchemical Molecular Binding

scientific article published on 16 November 2018

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

scientific article

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

scientific article published on 8 March 2018

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

scientific article (publication date: November 2015)

Asynchronous replica exchange for molecular simulations

scientific article

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

scientific article published on March 2015

Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses

scientific article

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

scientific article published on 09 March 2020

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

scientific article published on January 2012

Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: insights from NMR order parameters

scientific article published on January 2007

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

scientific article

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

scientific article published on May 2006

Correction: Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses

scientific article published on 27 September 2013

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

article

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

scientific article

Erratum to "Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for Enhanced Presentation of HIV-1 gp41 Epitopes".

scientific article published in May 2010

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

scientific article published on 4 November 2016

Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase

scientific article

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

scientific article published in August 2004

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

scientific article published on 30 September 2019

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

scientific article

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

scientific article published in January 2007

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

article

New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif

scientific article published on 10 September 2018

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

scientific article

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

scientific article

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

scientific article published on 01 September 2019

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

scientific article published on January 2008

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

scientific article

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

scientific article

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

scientific article published on 01 October 2019

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

scientific article published on March 1, 2012

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

scientific article

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

scientific article published on 15 April 2016

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

scientific article published in April 2005

The AGBNP2 Implicit Solvation Model.

scientific article

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

scientific article

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

scientific article published in April 2002

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

scientific article published on 01 July 2019

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

scientific article published on 31 October 2011

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

scientific article published in April 2012

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

scientific article

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