The IGBB is a member of the NIH-funded Mississippi IDeA Network of Biomedical Research Excellence (Mississippi INBRE or MS-INBRE), a program designed to build biomedical infrastructure throughout the state. Through MS-INBRE, Mississippi students and faculty at Mississippi's undergraduate institutions are (1) trained in biomedical research techniques, (2) given the opportunity to work with top researchers at Mississippi's major research universities, (3) afforded access to state-of-the-art bioscience equipment, and (4) provided with assistance in preparing grant proposals. The IGBB serves as the MS-INBRE proteomics/computational biology core. For more information about MS-INBRE, click here.
Mahesh ChinthalapudiGraduate Research Associate
GRADUATE STUDENT
email(701) 373 6012
458 Dorman Hall
HPIDB - a unified resource for host-pathogen interactions
IGBB Authors:
Bindu Nanduri, Ranjit S. KumarPUBLICATION YEAR:
2010IMPACT FACTOR:
3.765CITATION COUNT:
130Kumar R, Nanduri B (2010) HPIDB - a unified resource for host-pathogen interactions.
BMC Bioinformatics 11(Suppl 6): S16.
DOI:
10.1186/1471-2105-11-S6-S16EID:
2-s2.0-77957719439PMID: 20946599
DOWNLOAD PDFABSTRACTBACKGROUND: 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.
The IGBB is supported, in part, by the following units:
The IGBB is an HPC² member center.
