PROCOGNATE statistics

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Protocols

PROCOGNATE specifications

Information


Unique identifier OMICS_24868
Name PROCOGNATE
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.6
Maintained No

Maintainer


This tool is not available anymore.

Additional information


https://www.ebi.ac.uk/thornton-srv/databases/procognate/help.html

Publication for PROCOGNATE

PROCOGNATE citations

 (3)
library_books

Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

2014
Sci Rep
PMCID: 5376175
PMID: 25220818
DOI: 10.1038/srep06356

[…] algorithm have already been extensively validated through use of appropriate datasets (PD and PM). Further, in this study a large-scale comparison with the crystallographically derived sites from the Procognate database has been carried out. In 2442 of 3209 complexes, a pocket at a similar location as well as the same ligand association is predicted. The entire site-based function annotation pipel […]

library_books

Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

2014
PLoS One
PMCID: 3885575
PMID: 24416252
DOI: 10.1371/journal.pone.0084623

[…] from the primary literature in the CSA were used.Ligand (substrate, cofactor, intermediate, products and their analogues) information in the Protein Data Bank (PDB) was obtained from the EzCatDB and PROCOGNATE (ver. 1.6) databases. All annotations in the EzCatDB and the cognate ligand entries with similarity scores higher than 0.5 in PROCOGNATE were used. Ligand binding residues were defined fro […]

call_split

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

2012
BMC Genomics
PMCID: 3303731
PMID: 22759653
DOI: 10.1186/1471-2164-13-S4-S5
call_split See protocol

[…] of the length of the corresponding protein sequence. The dataset contains 803 SASs with 482 disease related and 323 neutral.The presence of cognate ligands in each structure was determined using the Procognate database []. The cognate ligands deposited in this database are those involved in the biological function of the proteins. After this filtering we found that 35 proteins have bound/unbound […]

Citations

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PROCOGNATE institution(s)
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; King’s College London, Randall Division of Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, London, UK
PROCOGNATE funding source(s)
Supported by NIH grant (GM62414), US DOE under contract (W-31-109-ENG38); by the Medical Research Council in the form of a Training Fellowship in Bioinformatics for the period 2001 to 2005.

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