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Updated: Jun 21, 2026
09:30
Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Extension of partial atom-to-atom maps: uniqueness and algorithms
Marcos E González Laffitte1,2, Tieu-Long Phan3,4, Peter F Stadler5,6,7,8,9,10,11
1Center for Scalable Data Analytics and Artificial Intelligence Dresden-Leipzig (ScaDS.AI), Leipzig University, Humboldtstrasse 25, 04105, Leipzig, Saxony, Germany. marcos@bioinf.uni-leipzig.de.
Algorithms for Molecular Biology : AMB
|June 19, 2026
Summary
Atom-to-atom maps (AAMs) are crucial for chemical synthesis and metabolomics but are often missing. This study presents a graph-theoretic method using Imaginary Transition State (ITS) graphs to uniquely extend partial AAMs, enabling accurate reconstruction.
Area of Science:
- Computational Chemistry
- Graph Theory
- Cheminformatics
Background:
- Chemical reaction databases lack atom-to-atom correspondence, hindering synthesis planning and metabolomics.
- Accurate atom-to-atom maps (AAMs) are essential but difficult to compute due to quantum mechanical underpinnings.
Purpose of the Study:
- To develop a computational method for reconstructing AAMs.
- To identify conditions for unique AAM extension using graph theory.
Main Methods:
- Focusing on partial AAMs covering the reaction center.
- Utilizing Imaginary Transition State (ITS) graphs to represent AAMs.
- Solving constrained graph-isomorphism problems for AAM extension.
Main Results:
- Unique AAM extension is guaranteed if partial maps cover the reaction center.
- Method is generalized for reactions where hydrogen atoms are implicit.
- Benchmarking of computational tools for AAM reconstruction was performed.
Conclusions:
- The ITS graph framework provides a robust method for AAM reconstruction.
- Computational approaches can reliably determine AAMs, advancing chemical informatics applications.
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