Let’s get honest about sampling

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

(2011) Emilio Gallicchio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein−Ligand Complexes

(2011) John C. Faver 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

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pathway and mechanism of drug binding to G-protein-coupled receptors

(2011) Ron O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Limits of Free Energy Computation for Protein−Ligand Interactions

(2010) Kenneth M. Merz   Journal of Chemical Theory and Computation

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities

(2010) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Massively parallel computation of absolute binding free energy with well-equilibrated states

(2009) Hideaki Fujitani et al.   PHYSICAL REVIEW E

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

(2008) Yuqing Deng et al.   JOURNAL OF CHEMICAL PHYSICS