Fragment Finder: a web-based software to identify similar three-dimensional structural motif.

FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles (phi and ). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling.

CADB-2.0: Conformation Angles Database.

The Conformation Angles Data Base (CADB) is a comprehensive, authoritative and timely knowledge base with a powerful query engine developed to facilitate the retrieval of information related to the conformational angles (main chain and side chain) of the amino-acid residues present in non-redundant (both 25 and 90%) data sets. The updated version has improved options for determining the dependency of the conformation angles of a particular residue upon the flanking residues, doublet analysis, triplet analysis and analysis of a particular protein structure. It is worth mentioning that for all options a user-friendly and convenient Java graphical user interface (GUI) has been provided to display the output on the client machine.