A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule
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 de...
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1155/2014/286974 |
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| author | Hamza Hentabli Faisal Saeed Ammar Abdo Naomie Salim |
| author_facet | Hamza Hentabli Faisal Saeed Ammar Abdo Naomie Salim |
| author_sort | Hamza Hentabli |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-875a6de8c3a7448f90c0819f821541c9 |
| institution | Kabale University |
| issn | 2356-6140 1537-744X |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-875a6de8c3a7448f90c0819f821541c92025-02-03T05:51:21ZengWileyThe Scientific World Journal2356-61401537-744X2014-01-01201410.1155/2014/286974286974A New Graph-Based Molecular Descriptor Using the Canonical Representation of the MoleculeHamza Hentabli0Faisal Saeed1Ammar Abdo2Naomie Salim3Faculty of Computing, University Technology of Malaysia, 81310 Skudai, Johor, MalaysiaFaculty of Computing, University Technology of Malaysia, 81310 Skudai, Johor, MalaysiaComputer Science Department, Hodeidah University, Hodeidah, YemenFaculty of Computing, University Technology of Malaysia, 81310 Skudai, Johor, MalaysiaMolecular 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.http://dx.doi.org/10.1155/2014/286974 |
| spellingShingle | Hamza Hentabli Faisal Saeed Ammar Abdo Naomie Salim A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule The Scientific World Journal |
| title | A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule |
| title_full | A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule |
| title_fullStr | A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule |
| title_full_unstemmed | A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule |
| title_short | A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule |
| title_sort | new graph based molecular descriptor using the canonical representation of the molecule |
| url | http://dx.doi.org/10.1155/2014/286974 |
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