GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution
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- Kinjo Akira R.
- Institute for Protein Research, Osaka University
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- Nakamura Haruki
- Institute for Protein Research, Osaka University
抄録
Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results.<br>
収録刊行物
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- BIOPHYSICS
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BIOPHYSICS 8 (0), 79-94, 2012
日本生物物理学会
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キーワード
詳細情報 詳細情報について
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- CRID
- 1390282680198082176
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- NII論文ID
- 130002061589
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- COI
- 1:CAS:528:DC%2BC38Xpt1Wqu7s%3D
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- ISSN
- 13492942
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- Crossref
- CiNii Articles
- KAKEN
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- 抄録ライセンスフラグ
- 使用不可