Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches

Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules

(2019) Dario Vassetti et al.   Journal of Chemical Theory and Computation

Comment on “Statistical efficiency of methods for computing free energy of hydration” [J. Chem. Phys. 149, 144111 (2018)]

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution

(2019) Israel Cabeza de Vaca et al.   Journal of Chemical Theory and Computation

Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Myeloid Cell Leukemia 1 Inhibition: An in Silico Study Using Non-equilibrium Fast Double Annihilation Technology

(2018) Piero Procacci   Journal of Chemical Theory and Computation

SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach

(2018) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Statistical efficiency of methods for computing free energy of hydration

(2018) Ahmet Yildirim et al.   JOURNAL OF CHEMICAL PHYSICS

On the accurate estimation of free energies using the jarzynski equality

(2018) Mehrnoosh Arrar et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

(2018) Matteo Aldeghi et al.   ACS Central Science

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

(2017) Guilherme Duarte Ramos Matos et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules

(2017) Piero Procacci   Journal of Chemical Information and Modeling

Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

(2017) Piero Procacci et al.   Journal of Chemical Theory and Computation

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

(2017) Leela S. Dodda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

(2017) Zhao X. Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

(2016) Vytautas Gapsys et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

(2016) Piero Procacci   Journal of Chemical Information and Modeling

Accuracy limit of rigid 3-point water models

(2016) Saeed Izadi et al.   JOURNAL OF CHEMICAL PHYSICS

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

(2016) Brian K. Radak et al.   JOURNAL OF CHEMICAL PHYSICS

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

(2016) Francesca Nerattini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

(2015) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Design, Synthesis, and Protein Crystallography of Biaryltriazoles as Potent Tautomerase Inhibitors of Macrophage Migration Inhibitory Factor

(2015) Pawel Dziedzic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

(2014) Piero Procacci et al.   Journal of Chemical Theory and Computation

FreeSolv: a database of experimental and calculated hydration free energies, with input files

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Multiple Bennett acceptance ratio made easy for replica exchange simulations

(2013) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

(2012) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

(2011) Michael S. Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Let’s get honest about sampling

(2011) David L. Mobley   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide

(2010) Piero Procacci et al.   CHEMICAL PHYSICS

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

(2009) Simone Marsili et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Erratum: “Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration” [J. Chem. Phys. 122, 144107 (2005)]

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Length of Time’s Arrow

(2008) Edward H. Feng et al.   PHYSICAL REVIEW LETTERS