The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations

(2014) P. Bisignano et al.   Journal of Chemical Information and Modeling

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis

(2014) Adam T. Van Wart et al.   Journal of Chemical Theory and Computation

Foundations of Biomolecular Modeling

(2013) William L. Jorgensen   CELL

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Population Based Reweighting of Scaled Molecular Dynamics

(2013) William Sinko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

How Does a Drug Molecule Find Its Target Binding Site?

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

Pathway and mechanism of drug binding to G-protein-coupled receptors

(2011) Ron O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-lasting target binding and rebinding as mechanisms to prolong in vivo drug action

(2010) Georges Vauquelin et al.   BRITISH JOURNAL OF PHARMACOLOGY

Conformational Dynamics in Human Purine Nucleoside Phosphorylase with Reactants and Transition-State Analogues†

(2010) Jennifer S. Hirschi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Four generations of transition-state analogues for human purine nucleoside phosphorylase

(2010) M.-C. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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

A simple and fast algorithm for K-medoids clustering

(2008) Hae-Sang Park et al.   EXPERT SYSTEMS WITH APPLICATIONS

Single-sweep methods for free energy calculations

(2008) Luca Maragliano et al.   JOURNAL OF CHEMICAL PHYSICS

l-Enantiomers of Transition State Analogue Inhibitors Bound to Human Purine Nucleoside Phosphorylase

(2007) Agnes Rinaldo-Matthis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY