HADDOCK models of mutant protein complexes

HADDOCK models of mutant protein complexes gathered for the article: "C. Geng, A. Vangone, G.E. Folkers, L. Xue and Alexandre M.J.J. Bonvin, iSEE: Interface Structure, Evolution and Energy-based random forest predictor of binding affinity changes upon mutations. 2017. Submitted".


HADDOCK Protein-peptide models

HADDOCK protein-peptide models gathered for the article: "A unified conformational selection and induced fit approach to protein-peptide docking." Trellet M, Melquiond ASJ, Bonvin AMJJ. Mar 2013. PLoS One 8(3) dx.doi.org/10.1371/journal.pone.0058769


CAPRI round 30

This is a correction of the folder of CAPRI30 in the original SBgrid 221 dataset


Template-based Haddock models

THIS DATA IS ORIGINALLY USED IN XUE ET AL., BRIEFINGS IN BIOINFORMATICS, 2016: TEMPLATE-BASED PROTEIN-PROTEIN DOCKING EXPLOITING PAIRWISE INTERFACIAL RESIDUE RESTRAINTS by Li C Xue, Joao P.G.L.M. Rodrigues, Drena Dobbs, Vasant Honavar, Alexandre M.J.J. Bonvin


human O-GlcNAc transferase

MD trajectory. The coordinates of the OGT–UDP–peptide complex (PDB 3PE4) were optimized in the Protein Preparation Wizard (Schrodinger 2009) where hydrogens were added; water molecules, UDP and peptide were stripped; and the structure was minimized using the OPLS2001 forcefield. The 1-μm simulation used the CHARM27 forcefield46, and the simple point charge model for water47. The CHARM27 forcefield was applied to the system using the VIPARR utility. The default Desmond relaxation was performed before simulation, and molecular dynamics were run at constant temperature (300 K) and pressure (1 bar). The simulation was performed by using the program Desmond, version 2.2.9.1.030 compiled by SBGrid on an optimized 64-node Linux-based InfiniBand cluster and took 75 days to complete. Molecular dynamics trajectories were processed and animated with VMD48.


HADDOCK docking models

HADDOCK decoys for 55 new entries in Docking Benchmark 5