title: 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.
authors.affiliation: Toyota Technological Institute at Chicago, Illinois 60637, USA. j3xu@tti-c.org
authors.forename: Jinbo
authors.initials: J
authors.lastname: Xu
authors.forename: Jian
authors.initials: J
authors.lastname: Peng
authors.forename: Feng
authors.initials: F
authors.lastname: Zhao
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins