Evaluation of the coarse-grained OPEP force field for protein-protein docking

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

(2014) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody–Antigen Complexes

(2014) Gautier Robin et al.   JOURNAL OF MOLECULAR BIOLOGY

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

(2013) Ali May et al.   BIOINFORMATICS

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

(2013) Fabio Sterpone et al.   Journal of Chemical Theory and Computation

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

(2013) Shruthi Viswanath et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

(2012) Krishnakumar M. Ravikumar et al.   BIOPHYSICAL JOURNAL

The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energy design for protein-protein interactions

(2011) D. V. S. Ravikant et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem

(2010) Richard M. Jackson   PROTEIN SCIENCE

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Designing coarse grained-and atom based-potentials for protein-protein docking

(2010) Dror Tobi   BMC STRUCTURAL BIOLOGY

FRODOCK: a new approach for fast rotational protein–protein docking

(2009) José Ignacio Garzon et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Generic coarse-grained model for protein folding and aggregation

(2009) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY