title: Assessment of CASP11 contact-assisted predictions.
abstract: We present an overview of contact-assisted predictions in the eleventh round of critical assessment of protein structure prediction (CASP11), which included four categories: predicted contacts (Tp), correct contacts (Tc), simulated sparse NMR contacts (Ts), and cross-linking contacts (Tx). Comparison of assisted to unassisted model quality highlighted a relatively poor overall performance in CASP11 using predicted Tp and crosslinked Tx contact information. However, average model quality significantly improved in the correct Tc and simulated NMR Ts categories for most targets, where maximum improvement of unassisted models reached an impressive 70 GDT_TS. Comparison of the performance in the correct Tc category to CASP10 suggested the improvement in CASP11 model quality originated from an increased number of provided contacts per target. Group rankings based on a combination of scores used in the CASP11 free modeling (FM) assessment for each category highlight four top-performing groups, with three from the Lee lab and one from the Baker lab. We used the overall performance of these groups in each category to develop hypotheses for their relative outperformance in the correct Tc and simulated NMR Ts categories, which stemmed from the fraction of correct contacts provided (correct Tc category) and a reduced fraction of correct contacts offset by an increased coverage of the correct contacts (simulated NMR Ts category). Proteins 2016; 84(Suppl 1):164-180. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050. lkinch@chop.swmed.edu.
authors.forename: Lisa N
authors.initials: LN
authors.lastname: Kinch
authors.affiliation: Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.|Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.
authors.forename: Wenlin
authors.initials: W
authors.lastname: Li
authors.affiliation: Genome Center, University of California, Davis, California, 95616.
authors.forename: Bohdan
authors.initials: B
authors.lastname: Monastyrskyy
authors.affiliation: Genome Center, University of California, 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, Dallas, Texas, 75390-9050.|Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.|Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003198:Computer Simulation; D003432:Cross-Linking Reagents / Q000737:chemistry*; D030562:Databases, Protein; D007391:International Cooperation; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D011506:Proteins
keywords: CASP11; contact-assisted; protein structure prediction