Theory of binless multi-state free energy estimation with applications to protein-ligand binding

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

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

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

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

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2010) Emilio Gallicchio 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

Good Practices in Free-Energy Calculations

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

Basic ingredients of free energy calculations: A review

(2009) Clara D. Christ et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng 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