2012 Fiscal Year Final Research Report
Comparisons of three-dimensional structures of proteins using hierarchical models and regularization for between-protein variations
| Project/Area Number |
22500275
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Bioinformatics/Life informatics
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| Research Institution | Tottori University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
FUJIWARA Shin-ichi 鳥取大学, 医学部, 講師 (00362880)
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| Project Period (FY) |
2010 – 2012
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| Keywords | 統計数学 / 生体分子 / 蛋白質 |
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| Research Abstract |
A method for comparing protein structures was developed. We consider a collection of three-dimensional coordinates of multiple proteins in which each protein has multiple conformations. The method exploits this protein-conformation hierarchy, and is based on the mixed-effects models on between- and within-protein variability. The estimation procedure is that of the EM-algorithm, in which the individual deviations of proteins are estimated and restricted using maximum-a-posteriori estimatorsand L1-regularization. At each iteration of the algorithm, the superposition of conformations can be made using a usual singular-value-decomposition but for specializedcovariance matrices. The results of numerical tests indicate that the method can be effective for characterizing the structures of multiple proteins simultaneously.
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