Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method

Good Practices in Free-Energy Calculations

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

Unorthodox uses of Bennett's acceptance ratio method

(2009) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity

(2009) Payel Das et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

(2009) Mikolai Fajer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessment of Nonequilibrium Free Energy Methods

(2009) Benjamin P. Cossins et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough

(2009) Gerhard König et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

(2009) Jozef Hritz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

(2008) William L. Jorgensen et al.   Journal of Chemical Theory and Computation

Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes

(2008) Maik Goette et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

(2008) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY