2013/03/07 by Ana Luísa Teixeira, Ana L. Teixeira, João P. Leal +6
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Physics and Astronomy · #Analytical Chemistry and Chromatography #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Chemistry and Stereochemistry Studies #Computational Drug Discovery Methods #Computational Engineering #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Finance #and Science (cs.CE) #cs.CE #physics.chem-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1303.1724
arxiv created 2013/03/07 · openalex publication_date 2013/03/07 · arxiv updated 2013/03/08 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28
Stereoisomers have the same molecular formula and the same atom connectivity and their existence can be related to the presence of different three-dimensional arrangements. Stereoisomerism is of great importance in many different fields since the molecular properties and biological effects of the stereoisomers are often significantly different. Most drugs for example, are often composed of a single stereoisomer of a compound, and while one of them may have therapeutic effects on the body, another may be toxic. A challenging task is the automatic detection of stereoisomers using line input specifications such as SMILES or InChI since it requires information about group theory (to distinguish stereoisomers using mathematical information about its symmetry), topology and geometry of the molecule. There are several software packages that include modules to handle stereochemistry, especially the ones to name a chemical structure and/or view, edit and generate chemical structure diagrams. However, there is a lack of software capable of automatically analyzing a molecule represented as a graph and generate a classification of the type of isomerism present in a given atom or bond. Considering the importance of stereoisomerism when comparing chemical structures, this report describes a computer program for analyzing and processing steric information contained in a chemical structure represented as a molecular graph and providing as output a binary classification of the isomer type based on the recommended conventions. Due to the complexity of the underlying issue, specification of stereochemical information is currently limited to explicit stereochemistry and to the two most common types of stereochemistry caused by asymmetry around carbon atoms: chiral atom and double bond. A Webtool to automatically identify and classify stereochemistry is available at http://nams.lasige.di.fc.ul.pt/tools.php