The objective of this research is to investigate and develop computational and haptic interface techniques to facilitate the design of molecular docking and molecular assembly for computer-aided molecular design (CAMD). Nano-scale molecular docking and molecular assembly are vital for the discovery and development of medicines, nano-scale devices, and new materials. In this paper, a new method called NanoDAS (Nano-scale Docking and Assembly Simulator) is presented to determine the feasibility of a ligand molecule reaching the binding site of a receptor molecule. To improve the design of molecular docking process, effective user intervention is necessary and is introduced through the use of a 5-DOF (degrees of freedom) force-torque feedback Haptic device developed at our research lab. Through the force-torque feedback haptic interface, a user is able to feel the forces exerted on the ligand by the receptor and find a feasible path using the proposed NanoDAS. The user is also able to determine whether the ligand can actually dock into the receptor by considering its conformational changes using a proposed energy minimization algorithm. The developed techniques can be used in Computer-Aided Molecular Design (CAMD) and Computer-Aided Drug Design (CADD) applications. Computer implementations and practical examples of the proposed methods are also presented.
| Identifer | oai:union.ndltd.org:NCSU/oai:NCSU:etd-06292005-164846 |
| Date | 30 June 2005 |
| Creators | Lai-Yuen, Susana Karina |
| Contributors | Dr. Yahya Fathi, Dr. Christopher G. Healey, Dr. Yuan-Shin Lee, Dr. Donald W. Brenner, Dr. Ezat T. Sanii |
| Publisher | NCSU |
| Source Sets | North Carolina State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://www.lib.ncsu.edu/theses/available/etd-06292005-164846/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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