期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 86, 期 -, 页码 51-66出版社
WILEY
DOI: 10.1002/prot.25407
关键词
CASP; contact prediction; correlated mutations; co-variation; evolutionary coupling; de novo structure prediction
资金
- US National Institute of General Medical Sciences (NIGMS/NIH) [GM100482]
- FP7 WeNMR European e-Infrastructure project [261572]
- Horizon West-Life European e-Infrastructure project [675858]
- national GRID Initiative of Belgium
- national GRID Initiative of France
- national GRID Initiative of Italy
- national GRID Initiative of Germany
- national GRID Initiative of the Netherlands
- national GRID Initiative of Poland
- national GRID Initiative of Portugal
- national GRID Initiative of Spain
- national GRID Initiative of UK
- national GRID Initiative of South Africa
- national GRID Initiative of Malaysia
- national GRID Initiative of Taiwan
- US Open Science Grid
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM100482] Funding Source: NIH RePORTER
Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology-based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single-domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures.
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