title: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
abstract: BACKGROUND
  Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database.
  
  
  METHODS
  AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of ~90% and average precision of ~80%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of ~70% and average precision of ~30%, correctly localizing binding sites for small molecules in ~95% of its predictions.
  
  
  CONCLUSIONS
  The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/.
authors.affiliation: Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain. mmarti@cipf.es
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
authors.forename: Andrea
authors.initials: A
authors.lastname: Rossi
authors.forename: Fátima
authors.initials: F
authors.lastname: Al-Shahrour
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016001:Confidence Intervals; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins