Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures
Abstract
Substructural fragments are proposed as a simple and safe way to encode molecular structures in a matrix containing the occurrence of fragments of a given type. The knowledge retrieved from QSPR modelling can also be stored in that matrix in addition to the information about fragments. Complex supramolecular systems (using special bond types) and chemical reactions (represented as Condensed Graphs of Reactions, CGR) can be treated similarly. The efficiency of fragments as descriptors has been demonstrated in QSPR studies of aqueous solubility for a diverse set of organic compounds as well as in the analysis of thermodynamic parameters for hydrogen-bonding in some supramolecular complexes. It has also been shown that CGR may be an interesting opportunity to perform similarity searches for chemical reactions. The relationship between the density of information in descriptors/knowledge matrices and the robustness of QSPR models is discussed.
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Fragment descriptors or fingerprints can easily be generated for CGR.
“In particularly, fragment descriptors or fingerprints can easily be generated for CGR.144”
From QSAR without borders (2020) · cites this paper as [144]
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Singular value decomposition and least squares solutions
Golub, G. H., & Reinsch, C. (1970) · Numerische Mathematik · doi:10.1007/bf02163027 · Cited by 2,929 · see citing works
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- Authors
- Varnek, A., Fourches, D., Hoonakker, F., & Solov’ev, V. P.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Russian Academy of Sciences (RU)
- Corresponding author
- Varnek, A.
- Venue
- Journal of Computer-Aided Molecular Design
- Published
- 2005-09
- Volume
- 19
- Issue
- 9-10
- Pages
- 693-703
- ISSN
- 0920-654X (ISSN-L)
- 1573-4951
- OpenAlex
- W2059713851
- Cited by
- 208
- References
- 2
- Citations by year
- 2026: 2 · 2025: 12 · 2024: 13 · 2023: 16 · 2022: 11 · 2021: 21 · 2020: 14 · 2019: 11 · 2018: 14 · 2017: 14 · 2016: 7 · 2015: 14 · 2014: 10 · 2013: 10 · 2012: 7
- FWCI
- 4.46
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Computer-Aided Molecular Design (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Mathematics › Geometry and Topology › Graph theory and applications
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › History and advancements in chemistry
- Keywords
- molecular descriptors, QSPR, supramolecular complexes, chemical reactions, water solubility
- MeSH terms
- Computer Simulation, Hydrogen Bonding, Models, Chemical, Solubility, Thermodynamics, Water, Molecular Structure, Quantitative Structure-Activity Relationship, Macromolecular Substances
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