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首页> 外文学位 >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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Nano-scale molecular docking and assembly simulator (nanoDAS) with haptic force-torque rendering and energy minimization for computer-aided molecular design (CAMD).

机译：纳米级分子对接和组装模拟器（nanoDAS），具有触觉力转矩渲染和能量最小化功能，可用于计算机辅助分子设计（CAMD）。

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The objective of this research is to investigate and develop computational and haptic interface techniques to improve the search and design of molecular docking, and to facilitate the assembly of molecular components during molecular design. Nano-scale molecular docking and molecular assembly are vital for the discovery and development of medicines, nano-scale devices, and new materials. Molecular docking and molecular assembly processes consist of finding the feasible pathway, and the correct location and orientation between two molecules so that they can remain attached to each other. As one small molecule (ligand) approaches a larger molecule (receptor), the ligand may need to change its conformation until finding one with the lowest interaction energy. Moreover, for a given receptor molecule, a huge number of ligand molecules need to be searched and tested before a potentially active drug can be identified. Therefore, a fast and efficient method to determine the feasibility of the ligand to dock into the receptor is required.; In this paper, a new method called NanoDAS ( Nano-scale Docking and Assembly Simulator) is presented to determine the feasibility of a ligand reaching the binding site of a receptor. The developed NanoDAS generates a search tree using a potential field analysis method and a local search with randomization technique to identify feasible ligands for docking into a receptor in molecular docking, and to determine the feasibility of nano-scale assembly in molecular design applications.; To improve the design of molecular docking and assembly processes, effective users (i.e., scientists or designers) intervention is necessary. In this paper, a 5-DOF (degrees of freedom) force-torque feedback Haptic device is introduced to provide force-torque feedback to users. Through the force-torque feedback haptic interface, a user is able to feel the forces exerted on the ligand by the receptor, and to determine whether the ligand can actually dock into the receptor by considering its conformational changes and finding a feasible path using the proposed NanoDAS. An energy minimization algorithm has also been proposed to find low-energy molecular conformations in real-time.; A Two-phase algorithm is proposed to analyze the probability of a ligand to be docked or assembled into another molecule. The first phase determines the feasibility of a ligand to dock into a targeted binding site of a receptor using an iterative searching procedure. The second phase generates a probability graph to examine all the ligand's feasible paths to find the most likely docking path. The developed Two-phase algorithm can identify the ligands that, although feasible for the targeted binding site of the receptor, posses higher probability towards other binding site than the targeted one.; In this paper, computer implementations and practical examples are presented. The results show that the proposed techniques can significantly increase the searching efficiency in the molecular docking and molecular assembly processes. The developed techniques can be used in Computer-Aided Molecular Design (CAMD) and Computer-Aided Drug Design (CADD) applications.
机译：这项研究的目的是研究和开发计算和触觉接口技术，以改善分子对接的搜索和设计，并在分子设计过程中促进分子组件的组装。纳米级分子对接和分子组装对于药物，纳米级设备和新材料的发现和开发至关重要。分子对接和分子组装过程包括找到可行的途径以及两个分子之间的正确位置和方向，以便它们可以保持彼此连接。当一个小分子（配体）接近一个大分子（受体）时，配体可能需要改变其构象，直到找到具有最低相互作用能的配体为止。此外，对于给定的受体分子，需要先搜索和测试大量配体分子，然后才能鉴定出潜在的活性药物。因此，需要一种快速有效的方法来确定配体对接入受体的可行性。在本文中，提出了一种新方法，称为NanoDAS（纳米级对接和组装模拟器），用于确定配体到达受体结合位点的可行性。开发的NanoDAS使用势场分析法和随机化技术进行局部搜索，生成搜索树，以确定在分子对接中可以对接入受体的可行配体，并确定在分子设计应用中进行纳米级组装的可行性。为了改善分子对接和组装过程的设计，有效的用户（即科学家或设计者）干预是必要的。在本文中，介绍了一种5自由度（自由度）力转矩反馈触觉设备，可为用户提供力转矩反馈。通过力-扭矩反馈触觉界面，用户能够感觉到受体施加在配体上的力，并通过考虑构象变化并使用拟议的方法找到可行的路径，从而确定配体是否真的可以对接受体NanoDAS。还提出了一种能量最小化算法来实时发现低能量分子构象。提出了一种两阶段算法来分析配体对接或组装成另一个分子的可能性。第一阶段使用迭代搜索程序确定配体对接至受体的靶向结合位点的可行性。第二阶段生成概率图，以检查所有配体的可行路径以找到最可能的对接路径。发达的两阶段算法可以识别配体，尽管这些配体对于受体的目标结合位点而言是可行的，但与目标结合位点相比，它对其他结合位点的可能性更高。本文介绍了计算机实现和实际示例。结果表明，所提出的技术可以大大提高分子对接和分子组装过程中的搜索效率。所开发的技术可以用于计算机辅助分子设计（CAMD）和计算机辅助药物设计（CADD）应用中。

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