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

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Alchemical free energy methods for drug discovery: progress and challenges

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

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

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

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

(2011) Mauro Lapelosa et al.   Journal of Chemical Theory and Computation

New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

(2011) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Acyclic Cucurbit[n]uril Congeners Are High Affinity Hosts

(2010) Da Ma et al.   JOURNAL OF ORGANIC CHEMISTRY

Good Practices in Free-Energy Calculations

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

The AGBNP2 Implicit Solvation Model

(2009) Emilio Gallicchio 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

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

(2009) J. Peter Guthrie   JOURNAL OF PHYSICAL CHEMISTRY B

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

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

Host–guest complexations of local anaesthetics by cucurbit[7]uril in aqueous solution

(2009) Ian W. Wyman et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Critical assessment of methods of protein structure prediction-Round VIII

(2009) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) David L. Mobley et al.   STRUCTURE

Statistically optimal analysis of samples from multiple equilibrium states

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

Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding†

(2008) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Asynchronous replica exchange for molecular simulations

(2007) Emilio Gallicchio et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY