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.

Information about the secondary structure of a protein can be helpful in understanding its native folded state. In previous work, it was shown that the medium-range interactions predominate in all-alpha class and the long-range interactions predominate in all-beta class proteins. Based on this, in this work the performance of several structure prediction methods in different structural classes of globular proteins was analyzed. It was found that all the methods predict the secondary structures of all-alpha proteins more accurately than other classes.