Structure databases
The central point of the protein structure database is Protein Data Bank (PDB) which was started in late 1970' at the US Brookheaven National Laboratory. In 1999, the Research Collaboratory for Structural Bioinformatics (RSCB) was formed to manage the PDB. In 2003, an international collaboration among RSCB, MSD-EBI at Europe and PDBj in Japan was initiated to form wwPDB, and the Magnetic Resonance Data Bank (BMRB) joined wwPDN in 2006. Although RSCB is the main entry point to access macromolecular structures, we may also find protein structures through the NCBI Entrez system and the EBI MSDLite server.
Main portals for the protein structures database
- RSCB - The main repository of macromolecular structures maintained by the Research Collaboration for Structural Bioinformatics.
- MMDB - The macromolecular database maintained by NCBI.
- MSD - The entry point for the EBI macromolecular structure database.
- MSDLite - The EBI web server providing simple search of protein structures.
- PDBSUM - The EBI web server which provides overview, schematic diagrams and interactions of structure.
- BMRB - The biological magnetic resonance data bank maintained at University of Wisconsin-Madison.
- ModBase - The database of comparative protein structure models developed and maintained at University of California, San Francisco.
Classification of the protein structures
- SCOP - The database of Structure Classification of Proteins developed and maintained by Cambridge University.
- CATH - The database of Calcification, Architecture, Topology and Homologous superfamily developed and maintained by University College, London.
Visualization of protein structures
- JenaLib - The Jena Library of Biological Macromolecules which provides information on macromolecular structures with an emphasis on visualization and analysis.