Biological Structure Databases

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Revision as of 09:30, 13 September 2008

BIOLOGICAL STRUCTURE DATABASES

A biological database is a large, organized body of persistent biological data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

There are various types of databases:

-Sequence Databases

-Structure Databases

MACROMOLECULAR 3D STRUCTURE DATABASES

RCSB PDB : http://www.rcsb.org/pdb/home/

MMDB: http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

EBI structure databases: http://www.ebi.ac.uk/Databases/structure.html

PSdB: http://www.daviddeerfield.com/PSdb/

CATH: http://www.cathdb.info/

SCOP: http://Scopes-lmb.cam.ac.uk/scop/

SWISS-3D IMAGE: http://expasy.org/sw3d/

SWISS-MODEL: http://swissmodell.expasy.org//SWISSMODEL.html

ModBase: http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

RCSB PDB

The RCSB PDB contains 3-D biological macromolecular structure data from X-ray crystallography, NMR, and Cryo-EM. It is operated by Rutgers, The State University of New Jersey and the San Diego Supercomputer Center at the University of California, San Diego. The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.

MMDB

NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Protein Data Bank (),PDB excluding theoretical models. MMDB is a database of ASN.1-formatted records. It was designed for flexibility, and as such, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy (surface models).

EBI structure databases

1) MSD(macromolecular structure databases) The Macromolecular Structure Database is a European project for the collection, management and distribution of data about macromolecular structures. It is responsible for the deposition and validation of new protein structures. It includes PDB search tools.

2) CSA(Catalytic Site Atlas) The Catalytic Site Atlas is a resource of catalytic sites and residues identified in enzymes using structural data.

3) DSSP The DSSP database is a database of secondary structure assignments (and much more) for all of the entries in the Protein Data Bank (PDB).

4) HSSP(homology-derived structures of proteins) HSSP is a derived database merging structural (2-D and 3-D) and sequence information (1-D).

5) PDBsum PDBsum is a pictorial database providing an at-a-glance overview of every macromolecular structure (nucleic acids and proteins) deposited in the Protein Data Bank (PDB).

PSdB(Protein Structure Database)

The Protein Structure Database (PSdb), is a protein database, derived from the information available in the Protein Databank and NRL-3D database, that relates secondary (e.g. Helix, Sheet, Turn, Random Coil) and tertiary information (e.g. Solvent accessibility, internal relative distances, and ligand interactions) to the primary structure.

CATH

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels : Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis.

SCOP: Structural Classification of Proteins

The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

SWISS-3D IMAGE

It is an image database which strives to provide high quality pictures of biological macromolecules with known three-dimensional structure. The database contains mostly images of experimentally elucidated structures, but also provides views of well accepted theoretical protein models.

SWISS-MODEL

SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

ModBase

It is a database of annotated comparative protein structure models, and associated resources. MODBASE contains theoretically calculated models, not experimentally determined structures.

More links to biological databases

1) http://www.science.co.il/Biomedical/Structure-Databases.asp 2) http://www.roseindia.net/bioinformatics/biologicaldatabases.shtml

Bioinformatics resources on the web

http://www.roseindia.net/bioinformatics/bioinformatics_resources.shtml

References

1.http://en.wikipedia.org/wiki/Genome_browser

2.http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

3.http://www.ebi.ac.uk/Databases/structure.html

4.http://Scopes-lmb.cam.ac.uk/scop/

5.http://www.rcsb.org/pdb/home/home.do

6.http://www.cathdb.info/

7.http://www.daviddeerfield.com/PSdb/

8.http://swissmodell.expasy.org//SWISSMODEL.html

9.http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

10.http://expasy.org/sw3d/

11.http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

12.http://www.ebi.ac.uk/Databases/structure.html