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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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Improved algorithms for enumerating tree-like chemical graphs with given path frequency.

Yusuke Ishida¹, Liang Zhao, Hiroshi Nagamochi

¹Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Yoshida, Kyoto, Japan. yusukei@amp.i.kyoto-u.ac.jp

Genome Informatics. International Conference on Genome Informatics

|May 9, 2009

Summary

This summary is machine-generated.

This study enhances chemical graph enumeration by introducing new bounding operations, significantly speeding up the identification of non-isomorphic tree-like chemical structures with specific path frequencies.

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Area of Science:

Computational chemistry
Graph theory
Cheminformatics

Background:

Enumerating non-isomorphic chemical graphs is crucial for compound classification and design.
Existing methods use branch-and-bound algorithms with path frequency constraints.
Previous algorithms efficiently enumerate trees but can be improved.

Purpose of the Study:

To develop more efficient algorithms for enumerating tree-like chemical graphs.
To introduce novel bounding operations to reduce search space.
To improve upon existing methods for chemical structure identification.

Main Methods:

Introduced two new bounding operations: detachment-cut and H-cut.
Built upon existing branch-and-bound algorithms and graph theory results.
Implemented and compared algorithms using chemical compound data from KEGG LIGAND.

Main Results:

The new algorithms significantly reduce the search space compared to previous methods.
Computational experiments demonstrate a substantial speed improvement.
The proposed methods are much faster than Fujiwara et al.'s algorithms.

Conclusions:

The novel bounding operations effectively enhance the efficiency of chemical graph enumeration.
This work provides a faster approach for identifying chemical structures with specific properties.
The improved algorithms have potential applications in chemical compound design and analysis.