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) -

PDHc Core Scaffold structure from C. thermophilum

Structural model of the E3BP core, refined in a C2 symmetrized cryoEM map. E3BP showed a minimal fold, which is conserved, and can be found in various other E2 proteins from diverse acyl-transferases, including the 2-keto acid dehydrogenase family. Additionally, by fitting the structural models into an asymmetrically refined cryoEM map, we supply a structural model for the native core scaffold of the PDHc metabolon from C. thermophilum. Models were built and refined by COOT and PHENIX. To capture the transient interaction of lipoyl domain (LD) and the core structure during the transacetylase reaction, we docked the LDs of C. thermophilum, H. sapiens, and N. crassa to their respective core structure. HADDOCK parameter files are deposited to reproduce docking. The best docking solution of C. thermophilum was used to study the interaction by extensive MD simulations. Parameter files and results are also given, to reproduce these simulations.

Protein-protein structures

HADDOCK refined 3D structures from multiple datasets (BM5, MANY, DC, CAPRI), used for experiments in the DeepRank paper. 1.Renaud, N. et al. DeepRank: A deep learning framework for data mining 3D protein-protein interfaces. bioRxiv 2021.01.29.425727 (2021) doi:10.1101/2021.01.29.425727.

Dataset of TCR-pMHC docked models

This dataset comprises bound TCR-pMHC models for 44 TCR docking benchmark cases. These models were produced using four docking platforms - ClusPro, HADDOCK, LightDock and ZDOCK - as a comparative study of docking software performance in the context of TCR-pMHC modelling. Each docking case was provided to the software platforms along with varying levels of detail about the binding interface in the form of four docking scenarios, to assess how effectively each platform made use of this additional information to improve modeling accuracy. A manuscript reporting these results has been submitted for publication.

2-Oxo-acid Dehydrogenase Complex component proteins from C. thermophilum

Structural models of the E1 and E2 proteins of Pyruvate Dehydrogenase Complex (PDHc), 2-Oxoglutarate Dehydrogenase (OGDHc), and Branched-Chain alpha-Keto Acid Dehydrogenase Complex (BCKDHc), E3BP of PDHc and E3, shared among all three complexes. In addition, a cif-file of E1, E2, E3BP, and E3 of PDHc modeled from cryoEM data is provided. Models were generated by homology modeling using MODELLER and refined using HADDOCK webserver.

HADDOCK refined models of ACE2 with the bound RBD of SARS-CoV-2 Spike glycoprotein

242 structural models of human ACE2 variants with the bound RBD of SARS-CoV-2 Spike glycoprotein refined with HADDOCK2.2 (initial PDB: 6M17, 6M0J). The structural models include in human population naturally occurring variants of ACE2 (140), models of the mutants with reported effects on the recognition of RBD (39), and computational alanine scanning mutagenesis of ACE2-RBD interface (63). Moreover, all aforementioned ACE2 variants can be found as a structural models of ACE2-B(0)AT1 complex with the bound RBD, including all ions and structurally-important glycan molecules (initial PDB: 6M17).

Simulated X-ray Diffraction data from Lysozyme (PDB 1H87)

Simulated lysozyme data set - the diffraction images were generated by MLFSOM. The calculation of structure factors was based on the gadolinium derivative of tetragonal Hen Egg-White Lysozyme (PDB 1H87), all the alternative conformations of residues were removed.

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)

CAPRI round 30

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

Template-based Haddock models


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 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