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    Compare local pocket and global protein structure models by small structure patterns

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    Type
    Conference Paper
    Authors
    Cui, Xuefeng
    Kuwahara, Hiroyuki cc
    Li, Shuai Cheng
    Gao, Xin cc
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2015-09-29
    Online Publication Date
    2015-09-29
    Print Publication Date
    2015
    Permanent link to this record
    http://hdl.handle.net/10754/579601
    
    Metadata
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    Abstract
    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/
    Citation
    Cui, X., Kuwahara, H., Li, S. C., & Gao, X. (2015). Compare local pocket and global protein structure models by small structure patterns. Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB ’15. doi:10.1145/2808719.2808756
    Publisher
    Association for Computing Machinery (ACM)
    Journal
    Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15
    Conference/Event name
    BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics
    DOI
    10.1145/2808719.2808756
    Additional Links
    http://dl.acm.org/citation.cfm?doid=2808719.2808756
    ae974a485f413a2113503eed53cd6c53
    10.1145/2808719.2808756
    Scopus Count
    Collections
    Conference Papers; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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