Protein structure prediction in CASP6 using CHIMERA and FAMS
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Updated: Aug 15, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Mayuko Takeda-Shitaka1, Genki Terashi1, Daisuke Takaya1
1School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Abstract:
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.
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