Guidelines for the analysis of free energy calculations

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

(2014) Jacob I. Monroe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

(2013) Anita de Ruiter et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

Frontiers in free-energy calculations of biological systems

(2013) Christophe Chipot   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

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

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

(2011) Tri T. Pham et al.   JOURNAL OF CHEMICAL PHYSICS

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

(2011) Himanshu Paliwal et al.   Journal of Chemical Theory and Computation

Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation

(2011) Andrew S. Paluch et al.   Journal of Chemical Theory and Computation

Linear-scaling soft-core scheme for alchemical free energy calculations

(2011) Floris P. Buelens et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

(2010) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Good Practices in Free-Energy Calculations

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

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistically optimal analysis of samples from multiple equilibrium states

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

Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles

(2008) Francisco J. Martínez-Veracoechea et al.   JOURNAL OF PHYSICAL CHEMISTRY B