Chemical curation to improve data accuracy: recent development of the 3DMET database

Biophys Physicobiol. 2018 Apr 27;15:87-93. doi: 10.2142/biophysico.15.0_87. eCollection 2018.


We have developed a three-dimensional structure database of natural metabolites (3DMET). Early development of the 3DMET database relied on content auto-generated from 2D-structures of other chemical databases. From 2009, we began manual curation, obtaining new compounds from published works. In the process of curation, problems of digitizing 3D-structures from structure drawings of documents were accumulated. As the same as auto-generation, structure drawings should be also payed attention about stereochemistry. Our experiences in manual curation of 3DMET, as described herein, may be useful to others in this field of research and for the development of supporting systems of a chemical structure database. Manual curation is still necessary for proper database entry of the 3D-configurations of chiral atoms, a problem encountered frequently among natural products.

Keywords: absolute configuration; chemical curation; chirality; molecular docking; natural products.