The Human Protein Reference Database (HPRD) is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...

accessible through the

Internet The Internet (or internet) is the global system of interconnected computer networks that uses the Internet protocol suite (TCP/IP) to communicate between networks and devices. It is a '' network of networks'' that consists of private, pub ...

. It is closely associated with the premier

Indian Indian or Indians may refer to: Peoples South Asia * Indian people, people of Indian nationality, or people who have an Indian ancestor ** Non-resident Indian, a citizen of India who has temporarily emigrated to another country * South Asia ...

Non-Profit research organisation Institute of Bioinformatics (IOB),

Bangalore Bangalore (), officially Bengaluru (), is the capital and largest city of the Indian state of Karnataka. It has a population of more than and a metropolitan population of around , making it the third most populous city and fifth most ...

. This database is a collaborative output of IOB and the Pandey Lab of

Johns Hopkins University Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private university, private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hem ...

Overview

The HPRD is a result of an international collaborative effort between the Institute of Bioinformatics in Bangalore, India and the Pandey lab at

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 Online Mendelian Inheritance in Man (OMIM) database. The National Center for Biotechnology Information provides link to HPRD through its human protein databases (e.g. Entrez Gene, RefSeq protein pertaining to genes and proteins. This resource depicts information on human protein functions including protein–protein interactions,

post-translational modifications Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes ...

, 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–protein interaction and subcellular localization data from HPRD have been used to develop a human protein interaction network. Highlights of HPRD as follows: * From 10,000 protein–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. * More than 50% of molecules annotated in HPRD have at least one PPI and 10% have more than 10 PPIs. * Experiments for PPIs are broadly grouped into three categories namely in vitro, in vivo and

yeast two hybrid Two-hybrid screening (originally known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions (such as bindi ...

(Y2H). Sixty percent of PPIs annotated in HPRD are supported by a single experiment whereas 26% of them are found to have two of the three experimental methods annotated. * HPRD contains 18,000 manually curated PTMs data belonging to 26 different types.

Phosphorylation In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...

is the leading type of modification of protein contributing to 63% of PTM data annotated in HPRD.

Glycosylation Glycosylation is the reaction in which a carbohydrate (or ' glycan'), i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not al ...

proteolytic cleavage Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, ...

and

disulfide bridge In biochemistry, a disulfide (or disulphide in British English) refers to a functional group with the structure . The linkage is also called an SS-bond or sometimes a disulfide bridge and is usually derived by the coupling of two thiol groups. In ...

events are the next leading contributors of PTM data. * HPRD data is available for download in tab delimited and

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...

file formats. 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 content is freely available for anyone to download and use.

PhosphoMotif Finder

PhosphoMotif Finder 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

There are other databases that deal with human proteome (e.g. BioGRID, BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome). Each database has its own style of presenting the data. It is a difficult task for most investigators to compare the voluminous data from these databases in order to conclude strengths and weaknesses of each database. Mathivanan and colleagues tried to address this issue while analyzing protein data by asking various questions. This analysis will help biologists to choose among these databases based on their needs.

References

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External links

*http://www.humanproteinpedia.org *http://www.hprd.org Biological databases Online databases