title: INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.
abstract: We present the INTREPID web server for predicting functionally important residues in proteins. INTREPID has been shown to boost the recall and precision of catalytic residue prediction over other sequence-based methods and can be used to identify other types of functional residues. The web server takes an input protein sequence, gathers homologs, constructs a multiple sequence alignment and phylogenetic tree and finally runs the INTREPID method to assign a score to each position. Residues predicted to be functionally important are displayed on homologous 3D structures (where available), highlighting spatial patterns of conservation at various significance thresholds. The INTREPID web server is available at http://phylogenomics.berkeley.edu/intrepid.
authors.affiliation: Department of Computer Science, University of California, Berkeley, USA.
authors.forename: Sriram
authors.initials: S
authors.lastname: Sankararaman
authors.forename: Bryan
authors.initials: B
authors.lastname: Kolaczkowski
authors.forename: Kimmen
authors.initials: K
authors.lastname: Sjölander
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D020134:Catalytic Domain; D020407:Internet; D008958:Models, Molecular; D010802:Phylogeny; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D011506:Proteins