An Attempt to Classify Elementary Reactions on the Basis of TS Motifs.

IF 2.8 4区医学 Q3 CHEMISTRY, MEDICINAL

Molecular Informatics Pub Date : 2025-02-01 DOI:10.1002/minf.202400040

Kenji Hori, Yujiro Matsuo, Toru Yamaguchi, Kimito Funatsu

引用次数: 0

Abstract

Reactions commonly used in synthetic organic chemistry are named after their discoverers or developers. They are called the name reactions and generally consist of several elementary reactions. Quantum chemical calculations can optimize transition state (TS) structures of the elementary reactions. The geometrical feature of TS is called TS motif. We have constructed a database (QMRDB) with the TS motif information and have been continuing to accumulate them. In the present study, we extracted 102 elementary reactions from the QMRDB and attempted to classify them using the Kohonen self-organization map. As the results, all the TS motifs were clustered. By firing a target compound on a Kohonen map generated, we expect to be able to easily find the TS motifs most similar to the target.

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来源期刊

Molecular Informatics CHEMISTRY, MEDICINAL-MATHEMATICAL & COMPUTATIONAL BIOLOGY

CiteScore

7.30

自引率

2.80%

发文量

审稿时长

3 months

期刊介绍： Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010. Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation. The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.