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

DOI
  • Minai Ryoichi
    Department of Supramolecular Biology, Yokohama City University
  • Matsuo Yo
    Department of Supramolecular Biology, Yokohama City University

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説明

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

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詳細情報 詳細情報について

  • CRID
    1390282680240315776
  • NII論文ID
    130000251506
  • DOI
    10.11185/imt.5.471
  • ISSN
    18810896
  • 本文言語コード
    en
  • データソース種別
    • JaLC
    • CiNii Articles
  • 抄録ライセンスフラグ
    使用不可

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