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

molecular assembly;BioCAD;computer-aided molecular design;molecular docking;nanotechnology;haptics;energy minimization

Lai-Yuen, Susana Karina ; 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,Lai-Yuen, Susana Karina ; 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

University:North Carolina State University

关键词: molecular assembly;    BioCAD;    computer-aided molecular design;    molecular docking;    nanotechnology;    haptics;    energy minimization;   

Others  :  https://repository.lib.ncsu.edu/bitstream/handle/1840.16/3257/etd.pdf?sequence=1&isAllowed=y

美国|英语

来源: null

【 摘 要 】

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.