Pre-calculated protein structure alignments at the RCSB PDB website

Abstract

Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.

Availability and implementation: A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org

Contact: andreas@sdsc.edu; pbourne@ucsd.edu.

Fig. 1.

A new user interface for jCE and jFATCAT structure alignments allows the investigation of sequence and 3D structure relationships. Here, the alignment of two kinases, the Hepatocyte growth factor receptor PDB ID 3A4P and the Proto-Oncogene Tyrosine-Protein Kinase Receptor RET PDB ID 2X2K. If the structures contain ligands they are also superimposed and displayed. The coloring for the sequence representation of the structure alignment represents the sequence conservation: red: identical residues, orange: similar and grey: structurally equivalent, but sequence mismatch.