Improved flexible refinement of protein docking in CAPRI rounds 22-27

Charge Optimization Theory for Induced-Fit Ligands

(2012) Yang Shen et al.   Journal of Chemical Theory and Computation

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

(2012) Justyna Aleksandra Wojdyla et al.   JOURNAL OF MOLECULAR BIOLOGY

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein

(2011) Dominique Liger et al.   NUCLEIC ACIDS RESEARCH

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

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

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystal structure of the CBM22-1–GH10 modules complexed with xylohexaose

(2010) Shabir Najmudin et al.   JOURNAL OF STRUCTURAL BIOLOGY

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

(2010) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

(2009) A. Bakan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

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

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

(2008) Yang Shen et al.   PLoS Computational Biology