Current Challenges in Development of a Database of Three-Dimensional Chemical Structures
Identifieur interne : 000050 ( Main/Exploration ); précédent : 000049; suivant : 000051Current Challenges in Development of a Database of Three-Dimensional Chemical Structures
Auteurs : Miki H. Maeda [Japon]Source :
- Frontiers in Bioengineering and Biotechnology [ 2296-4185 ] ; 2015.
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.
Url:
DOI: 10.3389/fbioe.2015.00066
PubMed: 26075200
PubMed Central: 4443773
Affiliations:
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Maeda</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Biomolecular Research Unit, National Institute of Agrobiological Sciences</institution>,<addr-line>Tsukuba</addr-line>,<country>Japan</country></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Bioengineering and Biotechnology</title><idno type="eISSN">2296-4185</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bostrom, J" uniqKey="Bostrom J">J. Bostrom</name></author><author><name sortKey="Greenwood, J R" uniqKey="Greenwood J">J. R. Greenwood</name></author><author><name sortKey="Gottfries, J" uniqKey="Gottfries J">J. Gottfries</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Coles, S J" uniqKey="Coles S">S. J. Coles</name></author><author><name sortKey="Day, N E" uniqKey="Day N">N. E. Day</name></author><author><name sortKey="Murray Rust, P" uniqKey="Murray Rust P">P. Murray-Rust</name></author><author><name sortKey="Rzepa, H S" uniqKey="Rzepa H">H. S. Rzepa</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y. 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Weininger</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Maeda, Miki H" sort="Maeda, Miki H" uniqKey="Maeda M" first="Miki H." last="Maeda">Miki H. Maeda</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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