MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

(2011) Francesca Spyrakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient mapping of ligand migration channel networks in dynamic proteins

(2011) Tu-Liang Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

In Silico Prediction of Binding Sites on Proteins

(2010) Simon Leis et al.   CURRENT MEDICINAL CHEMISTRY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Ensemble Docking from Homology Models

(2010) Eva Maria Novoa et al.   Journal of Chemical Theory and Computation

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding

(2010) Angela M. Henzler et al.   Molecular Informatics

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin

(2009) Ayana Tomita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving Structure-Based Function Prediction Using Molecular Dynamics

(2009) Dariya S. Glazer et al.   STRUCTURE

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

MolAxis: Efficient and accurate identification of channels in macromolecules

(2008) Eitan Yaffe et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pocket extraction on proteins via the Voronoi diagram of spheres

(2007) Donguk Kim et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING