Molecular dynamics simulations and drug discovery

On understanding proton transfer to the biocatalytic [Fe―Fe]H sub-cluster in [Fe―Fe]H2ases: QM/MM MD simulations

(2011) G. Hong et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design

(2011) Jacob D. Durrant et al.   Chemical Biology & Drug Design

Alchemical free energy methods for drug discovery: progress and challenges

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

How Does a Drug Molecule Find Its Target Binding Site?

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

Computer-Aided Identification ofTrypanosoma bruceiUridine Diphosphate Galactose 4′-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness

(2010) Jacob D. Durrant et al.   JOURNAL OF MEDICINAL CHEMISTRY

Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome

(2010) Xiaoxia Ge et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

(2010) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1

(2010) Jacob D. Durrant et al.   PLoS Neglected Tropical Diseases

Computational Identification of Uncharacterized Cruzain Binding Sites

(2010) Jacob D. Durrant et al.   PLoS Neglected Tropical Diseases

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

A virtual screening study of the acetylcholine binding protein using a relaxed–complex approach

(2009) Arneh Babakhani et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

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

Accelerating molecular dynamic simulation on graphics processing units

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

Polarization effects in molecular mechanical force fields

(2009) Piotr Cieplak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Computational Study of the Mechanism and the Relative Free Energies of Binding of Anticholesteremic Inhibitors to Squalene-Hopene Cyclase†

(2008) Fabienne Schwab et al.   BIOCHEMISTRY

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Hit Identification and Binding Mode Predictions by Rigorous Free Energy Simulations

(2008) Julien Michel et al.   JOURNAL OF MEDICINAL CHEMISTRY

Optimization of Azoles as Anti-Human Immunodeficiency Virus Agents Guided by Free-Energy Calculations

(2008) Jacob G. Zeevaart et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei

(2008) R. E. Amaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA