Journal Article

KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites

Kensuke Nakamura, Naoki Shimura, Yuuki Otabe, Aki Hirai-Morita, Yukiko Nakamura, Naoaki Ono, Md Altaf Ul-Amin and Shigehiko Kanaya

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 54, issue 2, pages e4-e4
Published in print February 2013 | ISSN: 0032-0781
Published online January 2013 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcs186
KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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Studies on plant metabolites have attracted significant attention in recent years. Over the past 8 years, we have constructed a unique metabolite database, called KNApSAcK, that contains information on the relationships between metabolites and their expressing organism(s). In the present paper, we introduce KNApSAcK-3D, which contains the three-dimensional (3D) structures of all of the metabolic compounds included in the original KNApSAcK database. The 3D structure for each compound was optimized using the Merck Molecular Force Field (MMFF94), and a multiobjective genetic algorithm was used to search extensively for possible conformations and locate the global minimum. The resulting set of structures may be used for docking studies to identify new and potentially unexpected binding sites for target proteins. The 3D structures may also be utilized for more qualitative studies, such as the estimation of biological activities using 3D-QSAR. The database can be accessed via a link from the KNApSAcK Family website (http://kanaya.naist.jp/KNApSAcK_Family/) or directory at http://kanaya.naist.jp/knapsack3d/.

Keywords: Database; KNApSAcK; Species-metabolite relationship; Force field; Conformation analysis; 3D Pharmacophore

Journal Article.  3045 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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