Datasets from the Utrecht University



Models of protein-peptide complexes

Protein-cyclic peptides docking models obtained with HADDOCK corresponding to the optimal protocol described in: V. Charitou, S.C. van Keulen and A.M.J.J. Bonvin. A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4. J. Chem. Theo. and Comp. (2022) - https://doi.org/10.1021/acs.jctc.2c00075

ClustENM-HADDOCK pipeline models

PDBs, scores and RMSDs related with ClustENM-HADDOCK modelling pipeline for protein-protein and protein-DNA complexes

Docking models of antibody-antigen complexes

Antibody-antigen docking models gathered for the article: "Modelling of antibody-antigen complexes by information-driven docking." F. Ambrosetti, B. Jimenez-Garcia, J. Roel-Touris, A.M.J.J. Bonvin. Jun 2019. Structure.

Docking models for Docking Benchmark 4, 5 and CAPRI score_set

HADDOCK docking models for Protein-Protein Docking Benchmark 4; HADDOCK, pyDock, SwarmDock and ZDock docking models for new complexes of Docking Benchmark 5; Various docking models for CAPRI score_set. All of the non-HADDOCK models are refined with HADDOCK using energy minimisation.

HADDOCK models of mutant protein complexes

HADDOCK models of mutant protein complexes gathered for the article: "C. Geng, A. Vangone, G.E. Folkers, L.C. Xue and A.M.J.J. Bonvin. iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations. Proteins: Struc. Funct. & Bioinformatics 87, 110-119 (2019)."

HADDOCK membrane protein-protein complex models

Decoys of a membrane protein complex docking benchmark. The decoys were obtained after docking with the HADDOCK webserver (v2.2) and they belong in two sets which reflect two extreme docking scenarios. One where we would have no information about the nature of the interaction and we use random restraints to drive the docking, and one where we use restraints extracted from the interface of the native complex to drive the docking. We have generated 50800 structures for the first scenario, distributed in three stages: 50000, 400 and 400 for the rigid-body, simulated annealing and flexible refinement stages respectively. We have generated 10800 structures for the second scenario distributed in three stages: 10000, 400 and 400 for the rigid-body, simulated annealing and flexible refinement stages respectively.

HADDOCK-refined Biological/crystallographic protein-protein interfaces

HADDOCK refined models for the biological/crystallographic interfaces collected in the DC and MANY datasets

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

HADDOCK docking models

HADDOCK decoys for 55 new entries in Docking Benchmark 5