Super: A web server to rapidly screen superposable oligopeptide fragments from the protein data bank

James H. Collier, Arthur M. Lesk, Maria Garcia De La Banda, Arun S. Konagurthu

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

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 80500 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.

Original languageEnglish (US)
Pages (from-to)W334-W339
JournalNucleic acids research
Volume40
Issue numberW1
DOIs
StatePublished - Jul 2012

All Science Journal Classification (ASJC) codes

  • Genetics

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