- Human Protein Reference Database--2009 update. [PMID: 18988627]
T S Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C J Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K Kashyap, Riaz Mohmood, Y L Ramachandra, V Krishna, B Abdul Rahiman, Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, Akhilesh Pandey
Nucleic acids research 2009:37(Database issue)
1538 Citations (Google Scholar as of 2016-01-26)
Abstract: Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.
- Human protein reference database--2006 update. [PMID: 16381900]
Gopa R Mishra, M Suresh, K Kumaran, N Kannabiran, Shubha Suresh, P Bala, K Shivakumar, N Anuradha, Raghunath Reddy, T Madhan Raghavan, Shalini Menon, G Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K S Arun, Salil Sharma, K N Chandrika, Nandan Deshpande, Kshitish Palvankar, R Raghavnath, R Krishnakanth, Hiren Karathia, B Rekha, Rashmi Nayak, G Vishnupriya, H G Mohan Kumar, M Nagini, G S Sameer Kumar, Rojan Jose, P Deepthi, S Sujatha Mohan, T K B Gandhi, H C Harsha, Krishna S Deshpande, Malabika Sarker, T S Keshava Prasad, Akhilesh Pandey
Nucleic acids research 2006:34(Database issue)
575 Citations (Google Scholar as of 2016-04-18)
Abstract: Human Protein Reference Database (HPRD) (http://www.hprd.org) 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 (http://www.genprot.org), 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.
- Development of human protein reference database as an initial platform for approaching systems biology in humans. [PMID: 14525934]
Suraj Peri, J Daniel Navarro, Ramars Amanchy, Troels Z Kristiansen, Chandra Kiran Jonnalagadda, Vineeth Surendranath, Vidya Niranjan, Babylakshmi Muthusamy, T K B Gandhi, Mads Gronborg, Nieves Ibarrola, Nandan Deshpande, K Shanker, H N Shivashankar, B P Rashmi, M A Ramya, Zhixing Zhao, K N Chandrika, N Padma, H C Harsha, A J Yatish, M P Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Shubha Suresh, Neelanjana Ghosh, R Saravana, Sreenath Chandran, Subhalakshmi Krishna, Mary Joy, Sanjeev K Anand, V Madavan, Ansamma Joseph, Guang W Wong, William P Schiemann, Stefan N Constantinescu, Lily Huang, Roya Khosravi-Far, Hanno Steen, Muneesh Tewari, Saghi Ghaffari, Gerard C Blobe, Chi V Dang, Joe G N Garcia, Jonathan Pevsner, Ole N Jensen, Peter Roepstorff, Krishna S Deshpande, Arul M Chinnaiyan, Ada Hamosh, Aravinda Chakravarti, Akhilesh Pandey
Genome research 2003:13(10)
954 Citations (Google Scholar as of 2016-04-18)
Abstract: Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.