Dockground

Datasets of modeled structures of interacting individual proteins

Download Set 1
Select proteins from Set 1
How this set was generated
DOCKGROUND Help
This dataset contains modeled/distorted structures of 126 interacting proteins in 63 complexes from the DOCKGROUND X-ray Unbound Benchmark Set 3. For each unbound protein in the set, six models/distorted structures were generated with C-alpha RMSD from the native structure 1, 2, 3, 4, 5, and 6 Å. The structures were built by a combination of single-template homology modeling by NEST (Petrey et al, Proteins, 2003, 53: 430) and Nudget Elastic Band (NEB) technique (Elber & Karplus, Chem Phys Lett 1987, 139: 375). Entire dataset is downloadable as a single zipped archive (288 Mb). The models are stored in PDB format with the REMARK section containing the modeling parameters. A detailed description of each model is stored in PDF format. "Docking Benchmarks" section offers the possibility to select a subset of the models and download their PDB files in one gzipped archive. Detailed description available in Anischenko et al., Proteins 2014, 82(2):278-287 and in the info section.

Download Set 2
How this set was generated
DOCKGROUND Help
This dataset contains six modeled structures for each of 330 interacting proteins in 165 complexes manually selected from the DOCKGROUND X-ray Bound set at 30% sequence identity level. For each protein in the set, six models were generated with C-alpha RMSD from the native structure 1, 2, 3, 4, 5, and 6 Å. The structures were built by the stand-alone i-TASSER package from the Zhang's lab (Roy et al. Nat Protoc 2010, 5:725). The entire dataset is downloadable as a single zipped archive (55 Mb). The models are in PDB format. Detailed description is in the info section.

Download Set Q1
How this set was generated
DOCKGROUND Help
This dataset contains five models for each of 342 proteins (171 complexes) from the Dockground (http://dockground.compbio.ku.edu) docking benchmark set 4. The dataset was developed by Sternberg Lab at Imperial College London and Vakser Lab at the University of Kansas within the joint GWYRE (http://www.gwyre.org) project. The models of individual proteins were generated using the batch processing facility of the Phyre2 web server (Kelly et al., Nature Protocols 2015, 10:845-858) with accuracy assessed by the Phyre ranks (1 to 5). The models are stored in PDB format with the REMARK section containing the template information and the modeling parameters, i.e. confidence value, sequence similarity, etc. The entire dataset is downloadable as a single zipped archive.

Download Set Q2
How this set was generated
DOCKGROUND Help
This dataset contains five models for each of 1120 proteins (963 complexes) from the GWIDD (http://gwidd.compbio.ku.edu) database. The dataset was developed by Sternberg Lab at Imperial College London and Vakser Lab at the University of Kansas within the joint GWYRE (http://www.gwyre.org) project. The models of individual proteins were generated using the batch processing facility of the Phyre2 web server (Kelly et al., Nature Protocols 2015, 10:845-858) with accuracy assessed by the Phyre ranks (1 to 5). The models are stored in PDB format with the REMARK section containing the template information and the modeling parameters, i.e. confidence value, sequence similarity, etc. The entire dataset is downloadable as a single zipped archive.