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HPIDB - a unified resource for host-pathogen interactions
BACKGROUND: Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying h...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026363/ https://www.ncbi.nlm.nih.gov/pubmed/20946599 http://dx.doi.org/10.1186/1471-2105-11-S6-S16 |
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author | Kumar, Ranjit Nanduri, Bindu |
author_facet | Kumar, Ranjit Nanduri, Bindu |
author_sort | Kumar, Ranjit |
collection | PubMed |
description | BACKGROUND: Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens. RESULTS: Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database. CONCLUSIONS: HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at http://agbase.msstate.edu/hpi/main.html. |
format | Text |
id | pubmed-3026363 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30263632011-01-26 HPIDB - a unified resource for host-pathogen interactions Kumar, Ranjit Nanduri, Bindu BMC Bioinformatics Proceedings BACKGROUND: Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens. RESULTS: Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database. CONCLUSIONS: HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at http://agbase.msstate.edu/hpi/main.html. BioMed Central 2010-10-07 /pmc/articles/PMC3026363/ /pubmed/20946599 http://dx.doi.org/10.1186/1471-2105-11-S6-S16 Text en Copyright ©2010 Kumar and Nanduri; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Proceedings Kumar, Ranjit Nanduri, Bindu HPIDB - a unified resource for host-pathogen interactions |
title | HPIDB - a unified resource for host-pathogen interactions |
title_full | HPIDB - a unified resource for host-pathogen interactions |
title_fullStr | HPIDB - a unified resource for host-pathogen interactions |
title_full_unstemmed | HPIDB - a unified resource for host-pathogen interactions |
title_short | HPIDB - a unified resource for host-pathogen interactions |
title_sort | hpidb - a unified resource for host-pathogen interactions |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026363/ https://www.ncbi.nlm.nih.gov/pubmed/20946599 http://dx.doi.org/10.1186/1471-2105-11-S6-S16 |
work_keys_str_mv | AT kumarranjit hpidbaunifiedresourceforhostpathogeninteractions AT nanduribindu hpidbaunifiedresourceforhostpathogeninteractions |