title: Evaluation of free modeling targets in CASP11 and ROLL.
abstract: We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51-66. © 2015 Wiley Periodicals, Inc.
authors.affiliation: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050. lkinch@chop.swmed.edu.
authors.forename: Lisa N
authors.initials: LN
authors.lastname: Kinch
authors.affiliation: Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050.
authors.forename: Wenlin
authors.initials: W
authors.lastname: Li
authors.affiliation: Genome Center, University of California, 451 Health Sciences Drive, Davis, California 95616.
authors.forename: Bohdan
authors.initials: B
authors.lastname: Monastyrskyy
authors.affiliation: Genome Center, University of California, 451 Health Sciences Drive, Davis, California 95616.
authors.forename: Andriy
authors.initials: A
authors.lastname: Kryshtafovych
authors.affiliation: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050.|Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050.
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000737:chemistry; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003196:Computer Graphics; D030562:Databases, Protein; D006801:Humans; D007391:International Cooperation; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D014780:Viruses / Q000737:chemistry
chemical_list: D011506:Proteins
keywords: CASP ROLL; CASP11; ab initio; alignment quality; domain structure; free modeling; protein fold prediction; protein structure; structure comparison