Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank.
Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80,500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from: http://lcb.infotech.monash.edu.au/super.
Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia.
James H
JH
Collier
Arthur M
AM
Lesk
Maria
M
Garcia de la Banda
Arun S
AS
Konagurthu
D000465:Algorithms; D030562:Databases, Protein; D020407:Internet; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
D009842:Oligopeptides; D010446:Peptide Fragments