title: PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation.
abstract: PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane beta-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 A RMSD). The average PROTEUS2 prediction takes approximately 3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2.
authors.affiliation: Department of Computing Science and Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8.
authors.forename: Scott
authors.initials: S
authors.lastname: Montgomerie
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Cruz
authors.forename: Savita
authors.initials: S
authors.lastname: Shrivastava
authors.forename: David
authors.initials: D
authors.lastname: Arndt
authors.forename: Mark
authors.initials: M
authors.lastname: Berjanskii
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
mesh_terms: D000465:Algorithms; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D021382:Protein Sorting Signals; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D008565:Membrane Proteins; D021382:Protein Sorting Signals