Inference networks for molecular database similarity searching
Molecular similarity searching is a process to find chemical compounds that are similar to a target compound. The concept of molecular similarity play an important role in modern computer aided drug design methods, and has been successfully applied in the optimization of lead series. It is used for...
| Main Authors: | , |
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| Format: | Article |
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Computer Science Journals (CSC Journals)
2008
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| Online Access: | http://eprints.utm.my/8947/ |
| _version_ | 1848891780236312576 |
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| author | Abdo, Ammar Salim, Naomie |
| author_facet | Abdo, Ammar Salim, Naomie |
| author_sort | Abdo, Ammar |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | Molecular similarity searching is a process to find chemical compounds that are similar to a target compound. The concept of molecular similarity play an important role in modern computer aided drug design methods, and has been successfully applied in the optimization of lead series. It is used for chemical database searching and design of combinatorial libraries. In this paper, we explore the possibility and effectiveness of using Inference Bayesian network for similarity searching. The topology of the network represents the dependence relationships between molecular descriptors and molecules as well as the quantitative knowledge of probabilities encoding the strength of these relationships, mined from our compound collection. The retrieve of an active compound to a given target structure is obtained by means of an inference process through a network of dependences. The new approach is tested by its ability to retrieve seven sets of active molecules seeded in the MDDR. Our empirical results suggest that similarity method based on Bayesian networks provide a promising and encouraging alternative to existing similarity searching methods. |
| first_indexed | 2025-11-15T21:03:24Z |
| format | Article |
| id | utm-8947 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T21:03:24Z |
| publishDate | 2008 |
| publisher | Computer Science Journals (CSC Journals) |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | utm-89472018-03-07T21:04:42Z http://eprints.utm.my/8947/ Inference networks for molecular database similarity searching Abdo, Ammar Salim, Naomie QA75 Electronic computers. Computer science Molecular similarity searching is a process to find chemical compounds that are similar to a target compound. The concept of molecular similarity play an important role in modern computer aided drug design methods, and has been successfully applied in the optimization of lead series. It is used for chemical database searching and design of combinatorial libraries. In this paper, we explore the possibility and effectiveness of using Inference Bayesian network for similarity searching. The topology of the network represents the dependence relationships between molecular descriptors and molecules as well as the quantitative knowledge of probabilities encoding the strength of these relationships, mined from our compound collection. The retrieve of an active compound to a given target structure is obtained by means of an inference process through a network of dependences. The new approach is tested by its ability to retrieve seven sets of active molecules seeded in the MDDR. Our empirical results suggest that similarity method based on Bayesian networks provide a promising and encouraging alternative to existing similarity searching methods. Computer Science Journals (CSC Journals) 2008 Article PeerReviewed Abdo, Ammar and Salim, Naomie (2008) Inference networks for molecular database similarity searching. International Journal of Biometric and Bioinformatics, 2 (1). pp. 1-16. ISSN 1985-2347 http://www.cscjournals.org/Journals/IJBB/Volume2/Issue1/IJBB-2.pdf |
| spellingShingle | QA75 Electronic computers. Computer science Abdo, Ammar Salim, Naomie Inference networks for molecular database similarity searching |
| title | Inference networks for molecular database similarity searching |
| title_full | Inference networks for molecular database similarity searching |
| title_fullStr | Inference networks for molecular database similarity searching |
| title_full_unstemmed | Inference networks for molecular database similarity searching |
| title_short | Inference networks for molecular database similarity searching |
| title_sort | inference networks for molecular database similarity searching |
| topic | QA75 Electronic computers. Computer science |
| url | http://eprints.utm.my/8947/ http://eprints.utm.my/8947/ |