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

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. Proteins 2009. © 2009 Wiley‐Liss, Inc.