Virtual screening using molecular simulations

Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities

(2010) Cen Gao et al.   BIOPHYSICAL JOURNAL

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors

(2010) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Drug discovery: Pulled from a protein's embrace

(2010) William L. Jorgensen   NATURE

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

(2009) Dian Jiao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

(2009) Scott P. Brown et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular docking and ligand specificity in fragment-based inhibitor discovery

(2009) Yu Chen et al.   Nature Chemical Biology

Recent Developments in Fragment-Based Drug Discovery

(2008) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS