title: RANKPROP: a web server for protein remote homology detection.
abstract: We present a large-scale implementation of the Rankprop protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the Rankprop algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation.
  
  
  BACKGROUND
  The Rankprop web server and source code are available at http://rankprop.gs.washington.edu
authors.affiliation: NEC Laboratories of America, Princeton, NJ, USA. iain@nec-labs.com
authors.forename: Iain
authors.initials: I
authors.lastname: Melvin
authors.forename: Jason
authors.initials: J
authors.lastname: Weston
authors.forename: Christina
authors.initials: C
authors.lastname: Leslie
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D012372:ROC Curve; D040681:Structural Homology, Protein