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The Scientific World Journal
Volume 2014, Article ID 286974, 10 pages
Research Article

A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule

1Faculty of Computing, University Technology of Malaysia, 81310 Skudai, Johor, Malaysia
2Information Technology Department, Sanhan Community College, Sana’a, Yemen
3Computer Science Department, Hodeidah University, Hodeidah, Yemen

Received 21 January 2014; Revised 13 April 2014; Accepted 18 June 2014; Published 22 July 2014

Academic Editor: Vladimir Brusic

Copyright © 2014 Hamza Hentabli et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried.