Nano-scale Molecular Docking and Assembly Simulator (NanoDAS) with Haptic Force-Torque Rendering and Energy Minimization for Computer-Aided Molecular Design (CAMD)

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Title: Nano-scale Molecular Docking and Assembly Simulator (NanoDAS) with Haptic Force-Torque Rendering and Energy Minimization for Computer-Aided Molecular Design (CAMD)
Author: Lai-Yuen, Susana Karina
Advisors: Dr. Yahya Fathi, Committee Member
Dr. Christopher G. Healey, Committee Member
Dr. Yuan-Shin Lee, Committee Chair
Dr. Donald W. Brenner, Committee Member
Dr. Ezat T. Sanii, Committee Member
Abstract: 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.
Date: 2006-06-30
Degree: PhD
Discipline: Industrial Engineering
URI: http://www.lib.ncsu.edu/resolver/1840.16/3257


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