AltPS: A Structural Alignment Tool for Protein Surfaces Using Similarity of Local Atomic Environments

• Item type: Trans(1)
• 公開日: 2010-02-04
• タイトル: AltPS: A Structural Alignment Tool for Protein Surfaces Using Similarity of Local Atomic Environments
• タイトル / 言語: en
• タイトル: AltPS: A Structural Alignment Tool for Protein Surfaces Using Similarity of Local Atomic Environments
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: Database/Software Paper
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: Department of Supramolecular Biology, Yokohama City University / Presently with SINKEN Yamanashi Office
• 著者所属: Department of Supramolecular Biology, Yokohama City University / Presently with OncoTherapy Science, Inc.
• 著者所属(英): en
• 著者所属(英): Department of Supramolecular Biology, Yokohama City University / Presently with SINKEN Yamanashi Office
• 著者所属(英): en
• 著者所属(英): Department of Supramolecular Biology, Yokohama City University / Presently with OncoTherapy Science, Inc.
• 著者名: Ryoichi, Minai; Yo, Matsuo
• 著者名(英): Ryoichi, Minai; Yo, Matsuo
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: We have developed an alignment tool for comparing protein local surfaces (AltPS). This program enables efficient exhaustive searches of the entire protein surfaces, using a feature vector for a surface atom with 6 to 18 elements to describe the geometrical and physicochemical properties in the local environment, without referring sequence or fold homology. AltPS runs on a personal computer with the input of a pair of PDB coordinates and outputs similarity scores between identified similar surfaces, alignments of the surface atoms, and corresponding superposed coordinates, based on cluster analysis of similar surface regions. In this report, we present some results on the application of AltPS to several protein pairs with similar functions to identify similar functional sites. AltPS can be downloaded from http://d-search.atnifty.com/research.html
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: We have developed an alignment tool for comparing protein local surfaces (AltPS). This program enables efficient exhaustive searches of the entire protein surfaces, using a feature vector for a surface atom with 6 to 18 elements to describe the geometrical and physicochemical properties in the local environment, without referring sequence or fold homology. AltPS runs on a personal computer with the input of a pair of PDB coordinates and outputs similarity scores between identified similar surfaces, alignments of the surface atoms, and corresponding superposed coordinates, based on cluster analysis of similar surface regions. In this report, we present some results on the application of AltPS to several protein pairs with similar functions to identify similar functional sites. AltPS can be downloaded from http://d-search.atnifty.com/research.html
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12177013
• 書誌情報: IPSJ Transactions on Bioinformatics（TBIO）; 巻 3, p. 2-9, 発行日 2010-02-04
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-6679
• 出版者 / 言語: ja
• 出版者: 情報処理学会