Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Two-dimensional replica-exchange method for predicting protein-ligand binding structures

(2013) Hironori Kokubo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

(2012) Michael Deighan et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Protein–Ligand Binding Free Energies from Exhaustive Docking

(2012) Enrico O. Purisima et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Alchemical free energy methods for drug discovery: progress and challenges

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

Molecular Docking with Ligand Attached Water Molecules

(2011) Mette A. Lie et al.   Journal of Chemical Information and Modeling

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

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

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Let’s get honest about sampling

(2011) David L. Mobley   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

How Does a Drug Molecule Find Its Target Binding Site?

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

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Exchange Often and Properly in Replica Exchange Molecular Dynamics

(2010) Daniel J. Sindhikara et al.   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

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket

(2008) Wei Deng et al.   Journal of Chemical Information and Modeling

Investigation of MM-PBSA Rescoring of Docking Poses

(2008) David C. Thompson et al.   Journal of Chemical Information and Modeling

Statistically optimal analysis of samples from multiple equilibrium states

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

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY