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

Jinbo Xu, Jian Peng, Feng Zhao

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)133-137
Number of pages5
JournalProteins: Structure, Function and Bioinformatics
Volume77
Issue numberSUPPL. 9
DOIs
StatePublished - 2009

Keywords

  • CASP
  • Model quality assessment
  • Protein threading
  • Template-based modeling
  • Template-free modeling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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