Human protein reference database—2006 update

By Goparani Mishra, Mavanur R. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, Raghunath Reddy, T. M. Raghavan and 32 more. Nucleic Acids Res., 2005

2,341 citations recorded by the source corpus.

Human Protein Reference Database (HPRD) () was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein–protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein–protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/137832dd10d669a300b7751e0ed3e3b91172372a

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Citations in the corpus

MEMOTE for standardized genome-scale metabolic model testing (2020, neutral): “org/ (Prasad et al. 2009) InChI metabolite https://www.”
Structure-based prediction of protein-protein interactions on a genome-wide scale (2012, methodology): “For human, we used the databases: HPRD [32], DIP, BioGRID, MINT and IntAct, retrieving data deposited prior to Aug.”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, positive): “Subsequently, four additional datasets (WORM BioGRID, HUMAN HPRD, FLY BioGRID, and YEAST BioGRID) from two public databases [23,24], to which no confidence-based filtering have been applied (Materials and Methods, Table S1), were investigated for comparison.”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, background): “com), NetPath (http://www.netpath.org), IntAct (15) (data from small-scale experiments only), DIP (16), MINT (17), HPRD ( 18 ), BioGRID (19) and SPIKE (20).”
Characterising and Predicting Haploinsufficiency in the Human Genome (2010, background): “One is a binary protein-protein interaction network integrated from a number of sources [35–39].”
The UCSC Genome Browser Database: 2008 update (2007, background): “The hg18 Gene Sorter has been expanded to include the Wanker (37), Vidal (38) and Human Protein Reference Database (39) data sets showing the neighborhood of protein interactions surrounding selected genes.”
STRING 7—recent developments in the integration and prediction of protein interactions (2006, methodology): “…direct physical binding between proteins, numerous small-scale and high-throughput experiments have been undertaken, and most of their reported interactions are available from dedicated interaction databases (1–4), as well as from multipurpose databases centered on speciﬁc model organisms (5–7).”
Chapter 4: Protein Interactions and Disease (2012, background): “(i) Over 39,000 protein interactions have been identified in the human cell [70].”
Overview of the protein-protein interaction annotation extraction task of BioCreative II (2008, background): “Some interaction databases such as the human protein-protein interaction database HPRD (Human Protein Reference Database) [1], HomoMINT (inferred human network) [2], and MIPS (Munich Information Center for Protein Sequences) [3] focus on certain taxa and store mainly information for human or…”
GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S (2008, methodology): “The human experimental protein-protein interaction (PPI) data were derived from the Database of Interacting Proteins (DIP) (31), BioGrid (32), the Molecular Interaction Database (MINT) (33), the Biomolecular Interaction Network Database (BIND) (34), and the Human Protein Reference Database (HPRD) ( ”
NetPath: a public resource of curated signal transduction pathways (2010, methodology): “The pathways developed by us have been integrated with the Human Protein Reference Database (HPRD) [43,44].”