Sciences > Biology > Databases > Biochemistry Databases

See also Genome Projects

Alcohol Studies Database - (dead link)
" The database contains over 50,000 citations for journal articles, books, book chapters, dissertations, conference papers, and audio-visual material."
Rutgers University Center of Alcohol Studies

Blocks WWW Server - (dead link) "The blocks for the Blocks Database - (dead link) are made automatically by looking for the most highly conserved regions in groups of proteins documented in the Prosite Database. The Prosite pattern for a protein group is not used in any way to make the Blocks Database...A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA."

CAMPASS - (dead link)
CAMbridge database of Protein Alignments organised as Structural Superfamilies
Currently [May 2002] 5095 Protein Domains in 1067 superfamiles.
University of Cambridge - Dept. of Biochemistry

ChemBank Initiative for Chemical Genetics

  • Small Molecule Bioactives Database
    "The ChemBank Small Molecule Bioactives Database is a subproject under the ChemBank umbrella and is being worked on primarily by Jeremy Muhlich, Erik Brauner, Jim Conley, and Caroline Shamu."

Complex Carbohydrate Research Center

  • CCCR Spectral Databases - (dead link)
    Databases include: Proton NMR Spectra of Xyloglucans and the GC-EIMS of Partially Methylated Alditol Acetates.

DictyBase
An Online Informatics Resource for Dictyostelium
"The purpose of this site is to provide a centralized source for information about Dictyostelium discoideum and related organisms and to facilitate communication between researchers involved in studies of these fascinating organisms."

  • Franke Database of Dicty Literature
    "...is the continuing effort to compile all published references relating to Dictyostelium (related papers on Polysphondylium and other cellular slime molds are also included)."

Eukaryotic Promoter Database (EPD)
"...is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references."
By members of the the Bioinformatics Group of the ISREC (Swiss Institute for Experimental Cancer Research).

European Bioinformatics Institute

  • CluSTr
    "...(Clusters of SWISS-PROT+TrEMBL proteins) database offers an automatic classification of SWISS-PROT + TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART and TIGRFAMs. CluSTr also has cross-references to  HSSP and  PDB...is a useful resource for whole genome analysis and has already been used for the proteome analysis of a number of completely sequenced genomes. A preliminary proteome analysis was also produced for the human genome."

Image Library of Biological Macromolecules
"The library contains (hopefully) all RNA structures from the Protein Data Bank (PDB) and from the Nucleic Acid Database (NDB) and DNA structures and proteins."
IMB Jena Biocomputing Group

The Integrated Mycobacterial Database (MycDB) - (dead link)
Mmaintained by the Unite de Genetique Moleculaire Bacterienne at the Institut Pasteur in Paris and the Department of Biochemistry, Royal Institute of Technology in Stockholm

Klotho: Biochemical Compounds Declarative Database - (dead link) "Klotho is part of our attempt to model biological processes, beginning with biochemistry."

MEROPS Database - (dead link) "The MEROPS database provides a wealth of information on proteases. There is a page describing each individual protease as well as one for each of the families into which they can be grouped, and even for each of the clans into which the families can be grouped. Many hundreds of proteases can be found by name, identifier or the organism in which they occur...Access to the database is free for people in academic and government institutions. Workers in commercial organizations are expected to subscribe to a site licence."
Babraham Institute, near Cambridge, England

Molecular Database/Library
Includes their 3-D Virtual Chemistry Library with 150 molecules.

Protein Data Bank (PDB)
"...the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data."  As of 10 October 2001 holdings include 16245 structures.
Research Collaboratory for Structural Bioinformatics (RCSB)


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PubMed
"Bibliographic database containing citations for nearly 9 million biomedical articles from the National Library of Medicine's MEDLINE and pre-MEDLINE databases"

SWISS-PROT Database

University College London - Biomolecular Structure and Modelling Group

  • Enzyme Structures Database
    "This database contains the known enzyme structures that have been deposited in the Brookhaven Protein Data Bank (the PDB). There are currently 7432 PDB-enzyme entries in the PDB (as at 13 April 2001) involving 7109 separate PDB files - some files having more than one E.C. number associated with them."

UniProt - The Universal Protein Resource
"...is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR."

VirOligo Compilation Lab
"... is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place...To this end, we are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA) (2), microarray-based methods for hybridization and PCR amplification."
Dept. of Biochemistry and Molecular Biology, Oklahoma State University

WebMolecules - (dead link)
Maintained by the Molecular Arts Corporation


 



Maintained by Mike Madin.
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Academic Info