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
Data DOI: 10.15785/SBGRID/912 | Publication DOI: https://doi.org/10.1021/acs.jctc.2c00075 | Published: May 7, 2024
Bonvin Laboratory, Utrecht University
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.
Data DOI: 10.15785/SBGRID/848 | PDB ID 7OTT: RCSB PDBe | Published: Nov. 23, 2021
Kastritis Laboratory, Martin Luther University Halle-Wittenberg
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.
Data DOI: 10.15785/SBGRID/843 | Published: Oct. 28, 2021
Xue Laboratory, Radboud University Medical Center
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.
Data DOI: 10.15785/SBGRID/825 | Published: May 21, 2021
Chain Laboratory, University College London
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.
Data DOI: 10.15785/SBGRID/817 | PDB ID 7BGJ: RCSB PDBe | Published: Jan. 26, 2021
Kastritis Laboratory, Martin Luther University Halle-Wittenberg
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).
Data DOI: 10.15785/SBGRID/791 | Published: Aug. 21, 2020
Kastritis Laboratory, Martin Luther University Halle-Wittenberg
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.
Data DOI: 10.15785/SBGRID/746 | Published: May 29, 2020
Dohnalek Laboratory, Institute of Biotechnology of the Czech Academy of Sciences
PDBs, scores and RMSDs related with ClustENM-HADDOCK modelling pipeline for protein-protein and protein-DNA complexes
Data DOI: 10.15785/SBGRID/707 | Published: Sept. 27, 2019
Bonvin Laboratory, Utrecht University
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.
Data DOI: 10.15785/SBGRID/686 | Published: Sept. 27, 2019
Bonvin Laboratory, Utrecht University
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.
Data DOI: 10.15785/SBGRID/684 | Publication DOI: 10.1093/bioinformatics/btz496 | Published: July 9, 2019
Bonvin Laboratory, Utrecht University
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)."
Data DOI: 10.15785/SBGRID/651 | Publication DOI: 10.1002/prot.25630 | Published: July 9, 2019
Bonvin Laboratory, Utrecht University
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.
Data DOI: 10.15785/SBGRID/618 | Published: Oct. 29, 2018
Bonvin Laboratory, Utrecht University
HADDOCK refined models for the biological/crystallographic interfaces collected in the DC and MANY datasets
Data DOI: 10.15785/SBGRID/566 | Published: March 6, 2018
Bonvin Laboratory, Utrecht University
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".
Data DOI: 10.15785/SBGRID/520 | Published: Dec. 5, 2017
Bonvin Laboratory, Utrecht University
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
Data DOI: 10.15785/SBGRID/420 | Publication DOI: 10.1371/journal.pone.0058769 | Published: Jan. 24, 2017
Bonvin Laboratory, Utrecht University
This is a correction of the folder of CAPRI30 in the original SBgrid 221 dataset
Data DOI: 10.15785/SBGRID/261 | Publication DOI: 10.1093/bib/bbw027 | Published: April 26, 2016
Bonvin Laboratory, Utrecht University
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
Data DOI: 10.15785/SBGRID/221 | Publication DOI: 10.1093/bib/bbw027 | Published: March 9, 2016
Bonvin Laboratory, Utrecht University
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.
Data DOI: 10.15785/SBGRID/190 | PDB ID 3PE4: RCSB PDBe | Publication DOI: 10.1038/nature09638 | Published: Nov. 3, 2015
Sliz Laboratory, Harvard Medical School
HADDOCK decoys for 55 new entries in Docking Benchmark 5
Data DOI: 10.15785/SBGRID/131 | Published: May 26, 2015
Bonvin Laboratory, Utrecht University