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DOI:
Journal of Software:2006.17(zk):103-109

面向大分子的三维数据场特征分析与可视化
韩玮,汪莉,陈为,万华根,彭群生,吴韬,王琦
(浙江大学 CAD&CG国家重点实验室,浙江 杭州 310027;浙江大学 化学系 分子设计与分子热力学研究所,浙江 杭州 310027)
Feature Analysis and Visualization of 3D Scalar Field with the Applications to the Macromolecule
HAN Wei,WANG Li,CHEN Wei,WAN Hua-Gen,PENG Qun-Sheng,WU Tao,WANG Qi
()
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Received:March 15, 2006    Revised:September 11, 2006
> 中文摘要: 介绍了在面向生物大分子结构和功能分析的三维数据场建模、特征分析与可视化方面的初步尝试.从蛋白质分子结构出发,采用量子化学理论计算得到一个规则采样的三维数据场,场的每个格点上记录蛋白酶分子内部各种力的综合作用.在每个格点上实施离散一阶、二阶局部微分计算,从而筛选出一系列数据场内的临界点,这些临界点潜在地揭示了蛋白质分子的功能区域所在.继而,计算数据场内各种型值的分子势能面,交互地探寻具有一定生物活性的“通道”区域.此外,探索运用多种点、面和体可视化技术,来寻找分子内部的宏观结构.通过上述多种特征分析与可视化手段,成功地寻找到HIV-1蛋白酶分子中隐藏的水分子排出通道.
Abstract:This paper introduces the primary attempts on the modeling, analysis and visualization of the 3D macromolecular scalar field. According to the quantum chemical theory, one protein molecular structure is transformed into a regularly sampled 3D scalar field, in which each node records the combined effect of different actions in protease. By applying the first order and the second order local differential operators on individual node, a set of critical points which potentially depicts the active region of protein molecule are found. Also the paper gives some results after computing a sequence of molecular potential energy in the data field and interactively exploring the potential “tunnel” region exhibiting biological sense. In addition, the point-based, surface and volume rendering techniques are exploited to find the macro-structure inside the data field. With all these techniques, the escape route of water molecules hidden in the HIV-1 protease is successfully detected, which is in accordance with the experimental results.
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基金项目:Supported by the National Natural Science Foundation of China under Grant Nos.60533050, 60503056, 60021201 (国家自然科学 基金) Supported by the National Natural Science Foundation of China under Grant Nos.60533050, 60503056, 60021201 (国家自然科学 基金)
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韩 玮,汪 莉,陈 为,万华根,彭群生,吴 韬,王 琦.面向大分子的三维数据场特征分析与可视化.软件学报,2006,17(zk):103-109

HAN Wei,WANG Li,CHEN Wei,WAN Hua-Gen,PENG Qun-Sheng,WU Tao,WANG Qi.Feature Analysis and Visualization of 3D Scalar Field with the Applications to the Macromolecule.Journal of Software,2006,17(zk):103-109