ccPDB: compilation and creation of data sets from Protein Data Bank

Nucleic Acids Res. 2012 Jan;40(Database issue):D486-9. doi: 10.1093/nar/gkr1150. Epub 2011 Dec 1.

Abstract

ccPDB (http://crdd.osdd.net/raghava/ccpdb/) is a database of data sets compiled from the literature and Protein Data Bank (PDB). First, we collected and compiled data sets from the literature used for developing bioinformatics methods to annotate the structure and function of proteins. Second, data sets were derived from the latest release of PDB using standard protocols. Third, we developed a powerful module for creating a wide range of customized data sets from the current release of PDB. This is a flexible module that allows users to create data sets using a simple six step procedure. In addition, a number of web services have been integrated in ccPDB, which include submission of jobs on PDB-based servers, annotation of protein structures and generation of patterns. This database maintains >30 types of data sets such as secondary structure, tight-turns, nucleotide interacting residues, metals interacting residues, DNA/RNA binding residues and so on.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Databases, Protein*
  • Internet
  • Molecular Sequence Annotation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / physiology
  • Systems Integration

Substances

  • Proteins