Research Article | OPEN ACCESS
Retrieval Performance using Different Type of Similarity Coefficient for Virtual Screening
1Shereena Arif, 1Noor Zeemah Shamsheh Khan, 2Nurul Malim and 1Suhaila Zainudin
1Centre of Artificial Intelligence, Faculty of Information Sciences and Technology,
Universiti Kebangsaan Malaysia, 43650 UKM Bangi, Malaysia
2School of Computer Science, Universiti Sains Malaysia, 11800 Penang, Malaysia
Research Journal of Applied Sciences, Engineering and Technology 2015 5:391-395
Received: September 22, 2014 | Accepted: October 24, 2014 | Published: February 15, 2015
Abstract
Development of a new drug needs chemical databases as references to find lead compounds. This study aims to determine the best similarity coefficient to be used for virtual screening task using chemical databases. We calculated the structural resemblance between each pair of chemical structures in their own activity class to get the Mean Pairwise Similarity (MPS) value to see the nature of heterogeneity for each natural product and synthetic chemical databases. The process involves the 2D descriptor of type ECFC4 fingerprint to represent each structure and Tanimoto coefficient to calculate the similarity score between each pair of chemical structures in the same activity class. MPS for an activity class was obtained by taking the average of all similarity scores within that class. Next, three types of similarity coefficients have been used to calculate the similarity score between a query structure and each of the database structure. The results indicate that Tanimoto coefficient shows better performance compared to Russell Rao and Forbes in retrieval task using chemical database. This implies that Tanimoto coefficient is recommended to carry out virtual screening in drug development. More work should be carried out to determine the best combination of similarity coefficient and fingerprint type to get optimal retrieval performance.
Keywords:
Chemoinformatics, mean pairwise similarity, retrieval, similarity search , virtual screening,
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Competing interests
The authors have no competing interests.
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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
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