High throughput profile-profile based fold recognition for the entire human proteome

Background: In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry out these updates on demand is necessary to keep pace with the regular updates of sequence and structure databases. Providing the highest quality structural models requires the most intensive profile-profile fold recognition methods running with the very latest available sequence databases and fold libraries. However, running these methods on such a regular basis for every sequenced proteome requires large amounts of processing power. In this paper we describe and benchmark the JYDE (Job Yield Distribution Environment) system, which is a meta-scheduler designed to work above cluster schedulers, such as Sun Grid Engine (SGE) or Condor. We demonstrate the ability of JYDE to distribute the load of genomic-scale fold recognition across multiple independent Grid domains. We...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Liam J. McGuffin, Richard T. Smith, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones
• Keywords: BMCBI 2006, Fold Recognition, Fold Recognition Methods, Profile-profile Fold Recognition