title: SAM-T04: what is new in protein-structure prediction for CASP6.
abstract: The SAM-T04 method for predicting protein structures uses a single protocol across the entire range of targets, from comparative modeling to new folds. This protocol is similar to the SAM-T02 protocol used in CASP5, but has improvements in the iterative search for similar sequences in finding and aligning templates, in creating fragment libraries, in generating protein conformations, and in scoring the conformations. The automatic procedure made some improvements over simply selecting an alignment to the highest-scoring template, and human intervention made substantial improvements over the automatic procedure. The main improvements made by human intervention were from adding constraints to build (or retain) beta-sheets and from splitting multidomain proteins into separate domains. The uniform protocol was moderately successful across the entire range of target difficulty, but was somewhat less successful than other approaches in CASP6 on the comparative modeling targets.
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Kevin
authors.initials: K
authors.lastname: Karplus
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Sol
authors.initials: S
authors.lastname: Katzman
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: George
authors.initials: G
authors.lastname: Shackleford
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Martina
authors.initials: M
authors.lastname: Koeva
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Jenny
authors.initials: J
authors.lastname: Draper
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Bret
authors.initials: B
authors.lastname: Barnes
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Marcia
authors.initials: M
authors.lastname: Soriano
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
authors.forename: Richard
authors.initials: R
authors.lastname: Hughey
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D019281:Dimerization; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software