Human Protein Reference Database: Difference between revisions

Revision as of 03:00, 28 July 2010

Revision as of 13:38, 1 May 2011

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{{primarysources|date=November 2008}}

[[Image:HPRD.JPG|thumb|right|300 px|The HPRD provides a comprehensive link to any queried protein]]

The '''Human Protein Reference Database'''(HPRD) is a protein database accessible through the internet.<ref>Peri, S. ''et al.'' Development of human protein reference database as an initial platform for approaching systems biology in humans. ''Genome Research''. 2003. 13, 2363-23712363–71</ref>

The HPRD is a result of an international collaborative effort between the [http://www.ibioinformatics.org/ Institute of Bioinformatics] in Bangalore, India and the [http://pandeylab.igm.jhmi.edu/ Pandey lab] at [[Johns Hopkins University]] in Baltimore, USA. HPRD contains manually curated scientific information pertaining to the biology of most human proteins. Information regarding proteins involved in human diseases is annotated and linked to [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim Online Mendelian Inhertance in Man] (OMIM) database. The [http://www.ncbi.nlm.nih.gov/ National Center for Biotechnology Information] provides link to HPRD through its human protein databases (e.g. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Entrez Gene], [http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq protein]) pertaining to genes and proteins.

This resource depicts information on human protein functions including [[protein-proteinprotein–protein interactions]], [[post-translational modifications]], enzyme-substrate relationships and [[disease]] associations. Protein annotation information that is catalogued was derived through manual curation using published literature by expert biologists and through bioinformatics analyses of the protein sequence. The protein-proteinprotein–protein interaction and subcellular localization data from HPRD have been used to develop a human protein interaction network.<ref>Gandhi, T.K.B. ''et al.'' Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. ''Nature Genetics''. 2006. 3, 285-293285–293</ref>

Highlights of HPRD as follows:

• From 10,000 protein-proteinprotein–protein interactions (PPIs) annotated for 3,000 proteins in 2003, HPRD has grown to over 36,500 unique PPIs annotated for 25,000 proteins including 6,360 isoforms by the end of 2007.<ref>Mathivanan, S. ''et al.'' An evaluation of human protein-proteinprotein–protein interaction data in the public ___domain. ''BMC Bioinformatics''. 2006. 7, S19</ref>

• More than 50% of molecules annotated in HPRD have at least one PPI and 10% have more than 10 PPIs.

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• HPRD contains 18,000 manually curated PTMs data belonging to 26 different types. [[Phosphorylation]] is the leading type of modification of protein contributing to 63% of PTM data annotated in HPRD. [[Glycosylation]], [[proteolytic cleavage]] and [[disulfide bridge]] events are the next leading contributors of PTM data.

• HPRD data is available for download in tab delimited and [[XML]] file formats.<ref>Mishra, G. ''et al.'' Human protein reference database--2006database—2006 update. ''Nucleic Acids Research''. 2006. 34, 411-414411–414</ref>

HPRD also integrates data from [[Human Proteinpedia]], a community portal for integrating human protein data. The data from HPRD can be freely accessed and used by academic users while commercial entities are required to obtain a license for use. Human Proteinpedia<ref>Mathivanan, S. ''et al.'' Human Proteinpedia enables sharing of human protein data. ''Nature Biotechnology''. 2008. 26, 164-167164–167</ref> content is freely available for anyone to download and use.

==PhosphoMotif Finder==

PhosphoMotif Finder<ref>Amanchy, R. ''et al.'' A compendium of curated phosphorylation-based substrate and binding motifs. ''Nature Biotechnology''. 2007. 25, 285-286285–286</ref> contains known kinase/phosphatase substrate as well as binding motifs that are curated from the published literature. It reports the PRESENCE of any literature-derived motif in the query sequence. PhosphoMotif Finder does NOT PREDICT any motifs in the query protein sequence using any algorithm or other computational strategies.

== Comparison of protein data ==