MetalMine : a database of functional metal-binding sites in proteins
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概要
- 論文の詳細を見る
We present a new database called MetalMine that contains the classification of metal-binding sites derived from the structures of protein-metal-ion complexes. Metal-binding sites were automatically extracted from Protein Data Bank (PDB) structures, classified based on the protein domains in which the metal-binding sites are incorporated, and then manually curated. Tentative or artificial metal ion coordinations were excluded during this curation process. On the web pages of the database, the following information about metal-binding sites is presented in a hierarchical manner: the kind of metal ion, metal-binding site typically specified by the name of the protein, and each instance of metal-binding coordinates in the PDB structures. The database search engine currently supports the following two types of queries. First, given the PDB code of a protein–metal–ion complex, it provides a list of metal-binding sites incorporated in the structure file. Second, given an amino acid sequence as a query, it looks for matches with metal-binding residues in the Basic Local Alignment Search Tool (BLAST) sequence alignment. As of October 2009, MetalMine contained 412 classified entries of functional metal-binding sites, which we believe is the largest number of entries in databases available to the public.
- 2009-12-25
著者
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TAKAHASHI Hiroki
Graduate School of Information Science, Nara Institute of Science and Technology
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NAKAMURA Kensuke
Graduate School of Information Science, Nara Institute of Science and Technology
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ALTAF-UL-AMIN Md.
Graduate School of Information Science, Nara Institute of Science and Technology
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HIRAI Aki
Graduate School of Information Science, Nara Institute of Science and Technology
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Nakamura Kensuke
Graduate School Of Information Sci. Nara Inst. Of Sci. And Technol.
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Hashimoto T
Department Of Biotechnology Graduate School Of Engineering Osaka University
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Nakamura Kensuke
Graduate School Of Information Science Nara Institute Of Science And Technology
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Hirai Aki
Graduate School Of Information Science Nara Institute Of Science And Technology
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Altaf-ul-amin Md.
Graduate School Of Information Science Nara Institute Of Science And Technology
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Altaf‐ul‐amin Md.
Nara Institute Of Science And Technology Graduate School Of Information Science
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Takahashi Hiroki
Graduate School Of Human And Environmental Studies Kyoto University
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Takahashi Hiroki
Graduate School of Biomedical Engineering, Tohoku University, Sendai 980-8579, Japan
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