SwarmDock and the Use of Normal Modes in Protein-Protein Docking

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

(2010) Xiaofan Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4

(2009) Tatiana Isabet et al.   EMBO JOURNAL

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

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

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

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

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

(2008) Marc N Offman et al.   BMC STRUCTURAL BIOLOGY

Molecular docking with multi-objective Particle Swarm Optimization

(2007) Stefan Janson et al.   APPLIED SOFT COMPUTING

Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis

(2007) Tommy Sander et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING