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Protocols

DOCKGROUND specifications

Information


Unique identifier OMICS_09515
Name DOCKGROUND
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Ilya A. Vakser
  • person_outline Petras Kundrotas

Publications for DOCKGROUND

DOCKGROUND citations

 (8)
library_books

SnapDock—template based docking by Geometric Hashing

2017
Bioinformatics
PMCID: 5870628
PMID: 28881968
DOI: 10.1093/bioinformatics/btx233

[…] fragment. We also present a Flexible Template-Based Docking scheme, which allows hinge-based flexibility in one of the molecules. SnapDock was validated on the ZLAB 4.0 Docking Benchmark () using the Dockground () and PIFACE () template libraries. To mimic “real-life” large-scale docking, we applied SnapDock with the PIFACE library to model the interfaces of all the (non-redundant) complexes (some […]

library_books

Evaluation of the coarse grained OPEP force field for protein protein docking

2016
BMC Biophys
PMCID: 4839147
PMID: 27103992
DOI: 10.1186/s13628-016-0029-y

[…] To test the optimized rescoring function, we use the protein–protein complexes from the Dockground test set [], removing all complexes which are also in the ZDOCK Benchmark 4.0 and were already used for training. The remaining 74 complexes are listed in Table . As before, we perform unbo […]

library_books

Text Mining for Protein Docking

2015
PLoS Comput Biol
PMCID: 4674139
PMID: 26650466
DOI: 10.1371/journal.pcbi.1004630

[…] for structural prediction of the binding sites on proteins (existing approaches are for small non-protein ligands). The method was tested on PubMed abstracts of publications on protein complexes from Dockground (http://dockground.compbio.ku.edu) and showed a significant improvement of the docking success rates. […]

call_split

Structural neighboring property for identifying protein protein binding sites

2015
BMC Syst Biol
PMCID: 4565107
PMID: 26356630
DOI: 10.1186/1752-0509-9-S5-S3
call_split See protocol

[…] owest energy values. For conformational changed structures, our method calculates a set of possibly changed conformations of interfaces.As in [], we use a training set consisting of 79 complexes from Dockground [] to produce 79 SVM models, one for each complex, based on these energy items. Finally, we use trained SVM models to further select best 10 poses with lowest energy values for two input pr […]

library_books

Local Network Patterns in Protein Protein Interfaces

2013
PLoS One
PMCID: 3592891
PMID: 23520460
DOI: 10.1371/journal.pone.0057031

[…] at the profile constructed by the labeled 4-tuples was better able to identify the correct interface in 1KU6 than either the contact pairs or the contact triangles. On a data set of 15 complexes from DOCKGROUND, with 100 decoys each and 1–10 near-native complexes each, iScore achieved 83.6% specificity with 82% sensitivity. Although we do not intend to propose an advanced scoring function for prot […]

library_books

Correlation analysis of the side chains conformational distribution in bound and unbound proteins

2012
BMC Bioinformatics
PMCID: 3479416
PMID: 22984947
DOI: 10.1186/1471-2105-13-236

[…] The analysis was performed on the non-redundant Dockground Benchmark 3 set of bound and corresponding unbound protein structures []. The set consists of 233 complexes, with the unbound structures of both interacting proteins for 99 complexes, and t […]

Citations

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DOCKGROUND institution(s)
Center for Computational Biology, The University of Kansas, Lawrence, KS, USA; Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
DOCKGROUND funding source(s)
Supported by NIH grant R01GM074255 and NSF grants DBI1262621, DBI1565107 and CNS1337899.

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