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KNApSAcK-3D: a three-dimensional structure database of plant metabolites
Kensuke Nakamura1, Naoki Shimura, Yuuki Otabe
1Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-City, Gunma, Japan. skanaya@gtc.naist.jp
Plant & Cell Physiology
|January 8, 2013
Summary
KNApSAcK-3D is a new database providing 3D structures for plant metabolites. These structures aid in identifying protein binding sites and estimating biological activities for drug discovery.
Area of Science:
- Metabolomics
- Computational Chemistry
- Bioinformatics
Background:
- Plant metabolite research is growing.
- The KNApSAcK database links metabolites to organisms.
- There is a need for 3D structural data of metabolites.
Purpose of the Study:
- Introduce KNApSAcK-3D, a database of 3D metabolite structures.
- Provide optimized 3D conformations for compounds in KNApSAcK.
- Facilitate computational studies in plant metabolomics.
Main Methods:
- Utilized Merck Molecular Force Field (MMFF94) for structure optimization.
- Employed a multiobjective genetic algorithm to find global minimum conformations.
- Integrated existing KNApSAcK data with newly generated 3D structures.
Main Results:
- Generated and curated a comprehensive database of 3D metabolite structures.
- Optimized structures represent low-energy conformations.
- Database includes compounds from the KNApSAcK collection.
Conclusions:
- KNApSAcK-3D offers valuable 3D structural data for plant metabolites.
- The database supports docking studies for protein-ligand interactions.
- 3D structures enable 3D-QSAR for predicting biological activities.
