Pre-calculated protein structure alignments at the RCSB PDB website.
|Title||Pre-calculated protein structure alignments at the RCSB PDB website.|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE|
|Date Published||2010 Dec 1|
|Keywords||Algorithms, Amino Acid Sequence, Databases, Protein, Internet, Proteins, Software, Structural Homology, Protein, User-Computer Interface|
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 [at] sdsc.edu; pbourne [at] ucsd.edu.