PRRDB is a database of pattern recognition receptors and their ligands. The database is developed by Dr. Raghava's group at Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi.
Architecture of PRRDB
Aims & Objectives
Data Management at PRRDB
System Requirement to Access
Architecture [Table of contents]
Aims and Objectives [Table of contents]
The main aim of this database is to serve the academic community working in field of immunology (mainly subunit vaccine designing). This is a comprehensive database provides information about most of Pattern Recognition receptors and their ligands reported in literature. This information is essential as these ligands can be used as adjuvants along with the peptide vaccines to enhance their efficacy.
Data Management at PRRDB [Table of contents]
The database has a number of web tools that allow users to I) search any information about pattern recognition receptors and their ligands ii) browsing to rtrieve a class of compounds iii) BLAST search against related pattern recognition receptor proteins.
All data in PRRDB has been maintained in "Relational Database Management System" (RDBMS) called PostgreSQL which is a public domain software freely available to public. Full information about a peptide has been stored in a single table. Related information like reference, sequence has been stored in directories with internal links to main database.
* Publication Reference: The server consists brief information (e.g. title, years, name of journal and authors of paper) of source of entry which is link with ' Publication Reference' field of database.
* Sequence Databases: This server contain amino acid sequence of pattern recognition receptors, for further information these sequences have been hypertext linked with 'SWISSPROT' database.
* Medline Databse: PRRDB consists brief information (e.g. title, years, name of journal and authors of paper), and hypertext link to PubMed at NCBI.
System Requirement for Access [table of contents]
The PRRDB web server was developed in a UNIX environment on SUN server 420E in Solaris 7.0. This server is designed to provide easy access to the user, based upon a set of simple GUI (Graphical User Interface) forms. Methods for searching the databases and displaying the selected objects were built with a combination of Java Scripts, CGI-scripts in PERL 5.4.
System requirements for running the PRRDB System are :
o For PC, Windows 95 and above
o Internet Explorer 4.01 and above/Netscape 3.01 and above
Acknowledgements [Table of contents]
We use the following public domain programs in PRRDB:
o BLAST 2.04 of the NCBI Toolkit: Altschul, S.F., Madden, T.L., Schffer, A.A., Zhang, J., Zhang, Z., Miller, W. and D.J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402, 1997.
o Readseq Sequence conversion program : By D.G. Gilbert, Biology Dept. Indiana University, Bloomington, IN 47405, USA.
o Clustal W 1.7 : Thompson, J.D., Higgins, D.G. and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions- specific gap penalties and weight matrix I choice. Nucleic Acids Research, 22:4673-4680, 1994.
+ Mview - Brown, NP., Leroy C., Sander C. MView: A Web compatible database search or multiple alignment viewer. Bioinformatics 14: 380-381, 1998.