White Rose University Consortium logo
University of Leeds logo University of Sheffield logo York University logo

Comparison of chemical clustering methods using graph- and fingerprint-based similarity measures

Raymond, J.W., Blankley, C.J. and Willett, P. (2003) Comparison of chemical clustering methods using graph- and fingerprint-based similarity measures. Journal of Molecular Graphics and Modelling, 21 (5). pp. 421-433. ISSN 1093-3263

Full text available as:
[img]
Preview
Text
willettp4.pdf

Download (336Kb)

Abstract

This paper compares several published methods for clustering chemical structures, using both graph- and fingerprint-based similarity measures. The clusterings from each method were compared to determine the degree of cluster overlap. Each method was also evaluated on how well it grouped structures into clusters possessing a non-trivial substructural commonality. The methods which employ adjustable parameters were tested to determine the stability of each parameter for datasets of varying size and composition. Our experiments suggest that both graph- and fingerprint-based similarity measures can be used effectively for generating chemical clusterings; it is also suggested that the CAST and Yin–Chen methods, suggested recently for the clustering of gene expression patterns, may also prove effective for the clustering of 2D chemical structures.

Item Type: Article
Copyright, Publisher and Additional Information: Copyright © 2002 Elsevier Science Inc. This is an author produced electronic version of an article accepted for publication in Journal of Molecular Graphics and Modelling.
Keywords: Bit-string; Chemical graph; Chemical series; Clustering method; Fingerprint; Maximum common subgraph; Molecular similarity; Similarity
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield)
The University of Sheffield > University of Sheffield Research Centres and Institutes > The Krebs Institute for Biomolecular Research (Sheffield)
Depositing User: Repository Officer
Date Deposited: 15 Nov 2004
Last Modified: 05 Jun 2014 22:44
Published Version: http://www.elsevier.com/locate/JMGM
Status: Published
Refereed: Yes
Identification Number: 10.1016/S1093-3263(02)00188-2
URI: http://eprints.whiterose.ac.uk/id/eprint/170

Actions (repository staff only: login required)