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Updated: Jan 31, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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Published on: December 1, 2020

Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data.

Nora Beier¹, Thomas Gatter¹, Jakob L Andersen²

¹Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany.

Algorithms for Molecular Biology : AMB

|January 30, 2026

Summary

This summary is machine-generated.

The new laveau software generates explicit DPO rules and atom-to-atom maps from KEGG RCLASS data, enabling detailed atom-level models of metabolic networks.

Keywords:

Atom-to-Atom mapping Double push out rules Graph reconstruction Graph transformation KEGG Metabolic reactions RCLASS Reaction rules

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Area of Science:

Bioinformatics
Computational Chemistry
Systems Biology

Background:

Atom-to-atom maps are crucial for many applications but difficult to obtain.
KEGG reaction database uses RCLASSes, not direct atom-to-atom maps, hindering rule construction.
DPO graph transformation rules offer an efficient representation for atom-level mapping.

Purpose of the Study:

To develop a method for converting KEGG RCLASS data into DPO rules.
To enable the generation of explicit atom-to-atom maps from existing KEGG reaction data.

Main Methods:

Developed 'laveau', a tool to compute DPO rules from KEGG reactions and RCLASS data.
Algorithm translates RDM codes to RDM pattern graphs, merges them based on embeddings, and forms reactant/product subgraphs.
Atom-to-atom maps are derived from RDM codes to define DPO transformation rules.

Main Results:

laveau successfully generated 1232 DPO rules and 1594 atom-to-atom maps from 3195 RCLASSes.
The generated DPO rules applied to reactants yield complete atom-to-atom maps.
The tool effectively reconstructs atom-level details from RCLASS data.

Conclusions:

laveau software extracts local atom-to-atom maps from KEGG RCLASSes for enzyme-catalyzed reactions.
Provides DPO rules for atom-level metabolic network models, addressing a data gap.
Facilitates detailed analysis of biochemical transformations at the atomic level.