Comparisons of three-dimensional structures of proteins using hierarchical models and regularization for between-protein variations

使用分层模型和蛋白质间变异正则化比较蛋白质的三维结构

• 批准号: 22500275
• 负责人: AMISAKI Takashi
• 金额: $ 2.66万
• 依托单位: Tottori University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2010
• 资助国家: 日本
• 起止时间: 2010 至 2012
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22500275/
• 关键词: 統計数学; 生体分子; 蛋白質; 生体生命情報学

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.

开发了一种比较蛋白质结构的方法。我们考虑了多种蛋白质的三维坐标的集合，其中每种蛋白质具有多种构象。该方法利用了该蛋白质构成层次结构，并基于蛋白质之间和蛋白质内变异性的混合效应模型。估计过程是EM-金属的估计过程，其中使用最大A-posteriori估计值和L1-Regulination估算和限制了蛋白质的各个偏差。在算法的每次迭代中，构象的叠加都可以使用通常的单数值分解，但对于专门的covariance矩阵。数值测试的结果表明该方法可以有效地表征多种蛋白质的结构。

项目成果

Steric and Allosteric Effects of Fatty Acids on the Binding of Warfarin to Human Serum Albumin Revealed by Molecular Dynamics and Free Energy Calculations

• DOI: 10.1248/cpb.59.860
• 发表时间: 2011-07-01
• 期刊: CHEMICAL & PHARMACEUTICAL BULLETIN
• 影响因子: 1.7
• 作者: Fujiwara, Shin-ichi;Amisaki, Takashi
• 通讯作者: Amisaki, Takashi

Fatty acid binding to serum albumin: Molecular simulation approaches

• DOI: 10.1016/j.bbagen.2013.03.032
• 发表时间: 2013-12-01
• 期刊: BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
• 影响因子: 3
• 作者: Fujiwara, Shin-ichi;Amisaki, Takashi
• 通讯作者: Amisaki, Takashi