Protein structure prediction in CASP6 using CHIMERA and FAMS.
In CASP6, the CHIMERA-group predicted full-atom models of all targets using SKE-CHIMERA, a Web-user interface system for protein structure prediction that allows human intervention at necessary stages; we used a lot of information from our own data and from publicly available data. Using SKE-CHIMERA, we iterated manual step (template selection and alignment by the in-house program CHIMERA) and automatic step (three-dimensional model building by the in-house program FAMS). The official CASP6 assessment showed that CHIMERA-group was one of the most successful predictors in homology modeling, especially for FR/H (Fold Recognition/Homologous). In this article, we introduce the method of CHIMERA-group and discuss its successes and failures in CASP6.
Takeda-Shitaka
Mayuko
M
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Terashi
Genki
G
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Takaya
Daisuke
D
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Kanou
Kazuhiko
K
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Iwadate
Mitsuo
M
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Umeyama
Hideaki
H
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
D000465:Algorithms; D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D020407:Internet; 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
D019843:Archaeal Proteins; D001426:Bacterial Proteins