Construction of Database of Rat and Mouse Genes for Three Dimensional Monomer and Complex Protein Structure

三维单体和复杂蛋白质结构大鼠和小鼠基因数据库的构建

• 批准号: 18310139
• 负责人: UMEYAMA Hideaki
• 金额: $ 3.2万
• 依托单位: Kitasato University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2006
• 资助国家: 日本
• 起止时间: 2006 至 2007
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18310139/
• 关键词: Protein; Database; Rat; Mouse; FAMS; CASP; CAPRI; Complex; Structure Prediction; Interaction; Critical Assessment; Protein

In the first, we improved the performance of our Full Automatic Modeling System (FAMS) and Full Automatic Modeling System for protein complex (FAMS Complex). These modeling systems made it possible to predict accurate three-dimensional protein structures. The FAMS showed successful performance for prediction of protein three-dimensional structures in 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), which assessed the accuracy of modeling methods. Moreover the FAMS Complex performed well in Community wide experiment on the comparative evaluation of protein-protein docking for structure prediction (CAPRI).Secondarily, we developed the evaluation systems which evaluate quality of predicted protein structures and pairwise-alignments of amino acid sequences. These methods provide information of confidence of predicted models.Finally, we constructed huge protein structure modeling database of Rat and Mouse genes, and released as RIKEN FAMSBASE (http://famshelp.gsc.riken.jp/famsbase/) to the public. In the RIKEN FAMSBASE, any researchers can search three-dimensional protein structure models of Rat and Mouse genes from amino acid sequence, a Gene Name, and keywords.

首先，我们改进了我们的全自动建模系统（FAMS）和蛋白质复合物全自动建模系统（FAMS Complex）的性能。这些建模系统使得预测精确的三维蛋白质结构成为可能。FAMS在第七届蛋白质结构预测技术关键评估社区实验（CASP 7）中表现出成功的蛋白质三维结构预测性能，该实验评估了建模方法的准确性。此外，FAMS Complex在蛋白质-蛋白质对接结构预测（卡普里）的社区范围比较评价实验中表现良好。其次，我们开发了蛋白质结构预测和氨基酸序列配对比对的评价系统。最后，构建了大鼠和小鼠基因的蛋白质结构建模数据库，并以RIKEN FAMSBASE（http：//famshelp.gsc.riken.jp/famsbase/）的形式对外发布。在RIKEN FAMSBASE中，任何研究人员都可以从氨基酸序列，基因名称和关键字搜索大鼠和小鼠基因的三维蛋白质结构模型。

项目成果

Dynamic interaction among the platform domain and two membrane-proximal immunoglobulin-like domains of class I major histocompatibility complex : normal mode analysis

I类主要组织相容性复合物的平台结构域和两个近膜免疫球蛋白样结构域之间的动态相互作用：正常模式分析

• 发表时间: 2008
• 期刊: Chem. Pharm. Bull 56(5)
• 作者: Hiroyuki;Nojima;Mayuko;Takeda-Shitaka
• 通讯作者: Takeda-Shitaka

The SKE-DOC K server and human teams based on a combined meth od of shape complementarity and free energy estimatio n

SKE-DOC K 服务器和人类团队基于形状互补和自由能估计的组合方法

• 发表时间: 2007
• 期刊: Proteins 69(4)
• 作者: Genki;Terashi;Mayuko;Takeda-Shitaka
• 通讯作者: Takeda-Shitaka

The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation

基于形状互补和自由能估计组合方法的 SKE-DOCK 服务器和人员团队

• 发表时间: 2007
• 期刊: Proteins 69(4)
• 作者: Genki Terashi;Mayuko Takeda-Shitaka
• 通讯作者: Mayuko Takeda-Shitaka

Modeling of Protein Structures and Biomolecular Design

蛋白质结构建模和生物分子设计

• 发表时间: 2007
• 作者: Mitsuo;Iwadate
• 通讯作者: Iwadate

Identification of am ino acid residues of Salmonella S1yA that are critical for transcriptional regulation

沙门氏菌 S1yA 转录调控关键氨基酸残基的鉴定

• 发表时间: 2007
• 期刊: Microbiology 153
• 作者: Okada;N.;Oi;Y.;Takeda-Shitaka;M
• 通讯作者: M