Journal of Applied Crystallography

Volume 35, Part 5 (October 2002)

computer programs

J. Appl. Cryst. (2002). 35, 648-649 [ doi:10.1107/S002188980201292X ]

The PRIDE server for protein three-dimensional similarity

K. Vlahovicek, O. Carugo and S. Pongor

Abstract: The PRIDE server is an implementation of the PRIDE algorithm that compares protein three-dimensional structures in terms of their C distance distributions. In response to queries presented as single or concatenated Protein Data Bank (PDB) files, the server can carry out (i) a pairwise comparison of two protein three-dimensional structures, (ii) a structural clustering of protein three-dimensional structures, providing a distance matrix and a dendrogram as an output; and (iii) a similarity search with a protein domain structure query against the CATH database.

Keywords: World Wide Web server; internet tools; computer programs; macromolecular crystallography; protein crystallography; Protein Data Bank; database utilities.