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Abstract
We are developing a database named 3DMET, a three-dimensional structure database of natural metabolites. There are two major impediments to the creation of 3D chemical structures from a set of planar structure drawings: the limited accuracy of computer programs and insufficient human resources for manual curation. We have tested some 2D–3D converters to convert 2D structure files from external databases. These automatic conversion processes yielded an excessive number of improper conversions. To ascertain the quality of the conversions, we compared IUPAC Chemical Identifier and canonical SMILES notations before and after conversion. Structures whose notations correspond to each other were regarded as a correct conversion in our present work. We found that chiral inversion is the most serious factor during the improper conversion. In the current stage of our database construction, published books or articles have been resources for additions to our database. Chemicals are usually drawn as pictures on the paper. To save human resources, an optical structure reader was introduced. The program was quite useful but some particular errors were observed during our operation. We hope our trials for producing correct 3D structures will help other developers of chemical programs and curators of chemical databases.
Highlights
A database called 3DMET, a three-dimensional structure database of natural metabolites, is being developed in our laboratory
During the automatic conversion process by 3Dgenerator and energy minimization, we found excessive amounts of improper conversions (Maeda and Kondo, 2013)
Conversion from Picture to 2D Coordinates Compound pictures scanned from papers were extracted by CLiDE (Ibison et al, 1993) standard 5.2 with default parameters
Summary
A database called 3DMET, a three-dimensional structure database of natural metabolites, is being developed in our laboratory. 3D structures were converted from twodimensional (2D) structures of relevant external databases. New entries to 3DMET are collected from chemical structures from print form. The bottleneck in our project is curation. Because of the shortage of good curators, several trials for automatic operation were evaluated. All trials utilizing known programs indicated that their accuracy is insufficient
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