Evaluation Of Various Autodock Molecular Docking Programmes In Predicting The Neuraminidase Inhibitory Activity
| dc.contributor.author | RAIME, NURUL NADIA | |
| dc.date.accessioned | 2016-05-25T07:55:56Z | |
| dc.date.available | 2016-05-25T07:55:56Z | |
| dc.date.issued | 2015-10 | |
| dc.description.abstract | This study was done to evaluate the scoring and ranking of molecular docking programmes; AutoDock 3.0.5 (AD3), AutoDock 4.2 (AD4) and AutoDock Vina (ADVina) in predicting the inhibitory activity of neuraminidase inhibitor taken from NCI Diversity set II (DSII) and to compare those ranking and scoring with that of Genetic Optimization Ligand Docking (GOLD), as the gold standard for ranking. Then, validate this prediction with NA enzyme assay. There were two types of protein used; first set was against rigid protein and second set was against specified flexible residues of protein. Virtual screening of rigid NA protein was run against AD3, AD4 and ADVina, whilst flexible side chain of NA was run only against AD4 and ADVina. This was due to unavailable flexible side chain function in AD3 manual programme. Top 15 compounds from each set were further investigated with NA enzyme activity assays for its activity behaviour. Simultaneously, docking simulations with GOLD against top 15 compounds from each set were done to analyse its correlation status. The result showed screening of rigid NA protein using AD4 gave promising assay activity of 4 out of 15 compounds which have more than 50% inhibition (compound 37, 45, 49 and 51). Rigid NA protein against ADVina and AD3 gave two (compound 30, and 31) and three compounds (compound 5, 8, 16) with over 50% inhibition respectively. Docking with flexible residues of NA with ADVina resulted in 2 compounds with more than 50% inhibition (compound 20, and 31) and AD4 with no compound over 50% inhibition level. Compounds with more xxii than 50% inhibition activity were captured from different docking sets. Findings symbolized that each docking set capture ligand exclusively. However, based on the results, it showed no exclusive scaffold captured by distinguished docking software. Hence, there was no significant difference on top 15 selected compound constituents with more than 50% activity. | en_US |
| dc.identifier.uri | http://hdl.handle.net/123456789/2060 | |
| dc.subject | Evaluation Of Various Autodock Molecular Docking Programmes | en_US |
| dc.subject | In Predicting The Neuraminidase Inhibitory Activity | en_US |
| dc.title | Evaluation Of Various Autodock Molecular Docking Programmes In Predicting The Neuraminidase Inhibitory Activity | en_US |
| dc.type | Thesis | en_US |
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