SAM-T04: what is new in protein-structure prediction for CASP6.
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.
Karplus
Kevin
K
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Katzman
Sol
S
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Shackleford
George
G
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Koeva
Martina
M
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Draper
Jenny
J
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Barnes
Bret
B
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Soriano
Marcia
M
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
Hughey
Richard
R
Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, California.
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