A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database.
Chemical structure assignment
Crystallography Open Database
Molecular perception
PubChem
Journal
Journal of cheminformatics
ISSN: 1758-2946
Titre abrégé: J Cheminform
Pays: England
ID NLM: 101516718
Informations de publication
Date de publication:
19 Dec 2023
19 Dec 2023
Historique:
received:
28
08
2023
accepted:
09
11
2023
medline:
20
12
2023
pubmed:
20
12
2023
entrez:
20
12
2023
Statut:
epublish
Résumé
Knowledge about the 3-dimensional structure, orientation and interaction of chemical compounds is important in many areas of science and technology. X-ray crystallography is one of the experimental techniques capable of providing a large amount of structural information for a given compound, and it is widely used for characterisation of organic and metal-organic molecules. The method provides precise 3D coordinates of atoms inside crystals, however, it does not directly deliver information about certain chemical characteristics such as bond orders, delocalization, charges, lone electron pairs or lone electrons. These aspects of a molecular model have to be derived from crystallographic data using refined information about interatomic distances and atom types as well as employing general chemical knowledge. This publication describes a curated automatic pipeline for the derivation of chemical attributes of molecules from crystallographic models. The method is applied to build a catalogue of chemical entities in an open-access crystallographic database, the Crystallography Open Database (COD). The catalogue of such chemical entities is provided openly as a derived database. The content of this catalogue and the problems arising in the fully automated pipeline are discussed, along with the possibilities to introduce manual data curation into the process.
Identifiants
pubmed: 38115123
doi: 10.1186/s13321-023-00780-2
pii: 10.1186/s13321-023-00780-2
doi:
Types de publication
Journal Article
Langues
eng
Pagination
123Subventions
Organisme : Research Council of Lithuania
ID : MIP-23-87
Organisme : Research Council of Lithuania
ID : MIP-23-87
Organisme : Research Council of Lithuania
ID : MIP-23-87
Informations de copyright
© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
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