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Template-based and free modeling by RAPTOR++ in CASP8.

ABSTRACT: We developed and tested RAPTOR++ in CASP8 for protein structure prediction. RAPTOR++ contains four modules: threading, model quality assessment, multiple protein alignment, and template-free modeling. RAPTOR++ first threads a target protein to all the templates using three methods and then predicts the quality of the 3D model implied by each alignment using a model quality assessment method. Based upon the predicted quality, RAPTOR++ employs different strategies as follows. If multiple alignments have good quality, RAPTOR++ builds a multiple protein alignment between the target and top templates and then generates a 3D model using MODELLER. If all the alignments have very low quality, RAPTOR++ uses template-free modeling. Otherwise, RAPTOR++ submits a threading-generated 3D model with the best quality. RAPTOR++ was not ready for the first 1/3 targets and was under development during the whole CASP8 season. The template-based and template-free modeling modules in RAPTOR++ are not closely integrated. We are using our template-free modeling technique to refine template-based models.

SUBMITTER: Xu J

PROVIDER: S-EPMC2785131 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Template-based and free modeling by RAPTOR++ in CASP8.

Xu Jinbo J Peng Jian J Zhao Feng F

Proteins 20090101

We developed and tested RAPTOR++ in CASP8 for protein structure prediction. RAPTOR++ contains four modules: threading, model quality assessment, multiple protein alignment, and template-free modeling. RAPTOR++ first threads a target protein to all the templates using three methods and then predicts the quality of the 3D model implied by each alignment using a model quality assessment method. Based upon the predicted quality, RAPTOR++ employs different strategies as follows. If multiple alignment ...[more]

PMID: 19722267

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