title: CASP9 assessment of free modeling target predictions.
abstract: We present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) "Template free modeling" category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the "winner" of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as "meta predictors" by correctly selecting among models produced by the top-performing automated servers. The details of evaluation are available at http://prodata.swmed.edu/CASP9/ .
authors: Howard Hughes Medical Institute, University of Texas, Southwestern Medical Center, Dallas, TX 75390-9050, USA. . lkinch@chop.swmed.edu
authors: Lisa
authors: L
authors: Kinch
authors: Shuo
authors: S
authors: Yong Shi
authors: Qian
authors: Q
authors: Cong
authors: Hua
authors: H
authors: Cheng
authors: Yuxing
authors: Y
authors: Liao
authors: Nick V
authors: NV
authors: Grishin
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins