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AltPS: A Structural Alignment Tool for Protein Surfaces Using Similarity of Local Atomic Environments
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- Minai Ryoichi
- Department of Supramolecular Biology, Yokohama City University
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- Matsuo Yo
- Department of Supramolecular Biology, Yokohama City University
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Description
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
Journal
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- Information and Media Technologies
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Information and Media Technologies 5 (2), 471-478, 2010
Information and Media Technologies Editorial Board
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Details 詳細情報について
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- CRID
- 1390282680240315776
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- NII Article ID
- 130000251506
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- ISSN
- 18810896
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- Text Lang
- en
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- Data Source
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- JaLC
- CiNii Articles
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- Abstract License Flag
- Disallowed
