Computer Simulation of Interaction between Protein and Organic Molecules
| Autor: | Cheng-Chieh Wang, 王政傑 |
|---|---|
| Rok vydání: | 2011 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 99 Docking is one of the methods in virtual screeing. Studies from around 1980 to now, many docking software have been developed, but these software have many short comings. The software currently used for docking have many disadvantage: poor efficiency, rigid structure of the proteins and the ligands, poor accuracy, without the polarization after binding, leading virtual screening is still stuck in a supporting role. Our experiment with new method improves those shortcomings of docking. With this new method, we obtain the following improvements in docking process: better efficiency, flexible structure of the proteins and the ligands, better accuracy. In the depression-related protein docked with traditional Chinese medicine test. We change the conformations of ligands with the shapes of active sites before posing, this makes the conformation of complex much more reasonable, even more complicated, large ligands. In the experiment of random sites docking, we found a possible path for compounds traveling into active sites. We illustrate a docking area by linking all possible docking sites. The lead compound may not successfully travel into active site when this area is occupied by other proteins or ligands. In the docking experiment with side-chain rotation, we rotate the torsion angle to make side chains relax. We obtained a similar result with molecular dynamics, and saved a lot of time. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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