Databases

Bioinformatics Centre has several software Databases from general purpose to specific use. Some of these packages are developed at centre. BIC have number of public domain databases which are free for academic users. The academic users can download these public domain database from this site or from their orignal site. The databases at BIC include:

 

Databases available at BIC: BIC has procured a number of databases from various sources. Most of them is public domain which are free for academic users.

  • PROSITE

    • Prosite database is available on hard disk on lion.imtech.ernet.in in directory '/usr2/molmod/prosite'. Both data and documentation of sites are available in file prosite.d at and in prosite.doc respectively.

  • Rotamer Library

    • Backbone dependent rotamer library are available on harddisk of lion.imtech.ernet.in in directory '/usr2/molmod/bbdep/'.

  • Protein Data Bank (PDB)

    • PDB release 23.0, 1995 is avialable at centre which have all PDB file upto 1995.

  • ATLAS

    • ATLAS of protein and genomic sequences, release 56.00 June 31, 1998 is available. It consists PIR-Imternational and other databases.

  • GenBank

    • GenBank in flat file format is available at centre. BIC have release 95.0, June 15, 1996. It is in 4 CD's.

  • ENTREZ

    • It is a document retrieval system. Centre have release 23.0 june, 1996. It is in 6 CD's.

  • Medline CDs (1966-1997)

    • Consists the litrature in biosciences. BIC have Medline CD's from 1966 to 1977.

     

    Databases developed at the Centre: Number of databases were derived or created at the centre. The databases created at this centre include:

  • PSSD

    • Protein secondary structure database in compact form created for all proteins where structure (3-D) is known at resolution 3.2A or better.

  • RESTseq

    • A restriction enzyme database is created which have restriction enzymes and their recognition sequence and compatible to GMAP format.

  • CODONtab

    • A preferred codon usage for different host system has been created in format suitable for GMAP.

  • CONFangle

    • A program to generate phi, psi and chi from PDB files is developed. It can read PDB, AMBER, MOMOS, and GROMOS format coordinate files and output the angles of desired residues. The PDB database is avilable at the centre so the d atabase of conformation angle can be generate.

  • CAng Database

    • A program to generate phi, psi and chi from PDB files is developed. It can read PDB, AMBER, MOMOS, and GROMOS format coordinate files and output the angles of desired residues. The PDB database is avilable at the centre so the d atabase of conformation angle can be generate.

  • HPat Database

    • HPat consists the hydrogen bond pattern between backbone - backbone, backbone - sidechain, sidechain - sidechain atoms.

 

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