Using diffusion distances for flexible molecular shape comparison.
Using diffusion distances for flexible molecular shape comparison.
复制标题
使用扩散距离进行灵活的分子形状比较
DOI：
10.1186/1471-2105-11-480
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发表时间：
2010-09-24
影响因子：
3
通讯作者：
Benjamin W
中科院分区：
文献类型：
--
作者：
Liu YS;Li Q;Zheng GQ;Ramani K;Benjamin W
BackgroundMany molecules are flexible and exceeding significant shape deformations as part of their function，and yet most existing molecular shape comparison（MSC）methods treat them as rigid bodies，which may lead to increased shape recognition.ResultsIn this year，we present a new shape descriptor，named Diffusion Distance Shape Descriptor（DDSD），for comparison 3D shapes of flexible molecules.在我们的工作中，扩散距离被认为是在内部距离的意义上连接分子形状上的两个标志点的路径的平均长度。扩散距离对柔性形状变形，特别是拓扑变化具有鲁棒性，并且它很好地反映了分子结构和变形，而无需显式分解。我们的DDSD存储为直方图，这是分子表面上所有样本点对之间的扩散距离的概率分布。最后，灵活的MSC的问题减少到DDSD histographs.ConclusionsWe比较说明，DDSD是不敏感的柔性分子的形状变形，更有效地捕捉分子结构比传统的形状描述符。该算法具有鲁棒性，不需要任何柔性区域的先验知识。
BackgroundMany molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.ResultsIn this paper, we present a new shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D shapes of flexible molecules. The diffusion distance in our work is considered as an average length of paths connecting two landmark points on the molecular shape in a sense of inner distances. The diffusion distance is robust to flexible shape deformation, in particular to topological changes, and it reflects well the molecular structure and deformation without explicit decomposition. Our DDSD is stored as a histogram which is a probability distribution of diffusion distances between all sample point pairs on the molecular surface. Finally, the problem of flexible MSC is reduced to comparison of DDSD histograms.ConclusionsWe illustrate that DDSD is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. The presented algorithm is robust and does not require any prior knowledge of the flexible regions.
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影响因子：
4.3
作者：
Jain, Varun;Zhang, Hao
通讯作者：
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影响因子：
56.9
作者：
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通讯作者：
CONNOLLY, ML
DOI：
10.1109/tcbb.2006.43
发表时间：
2006-07-01
影响因子：
4.5
作者：
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通讯作者：
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DOI：
10.1109/tpami.2007.41
发表时间：
2007-02-01
影响因子：
23.6
作者：
Ling, Haibin;Jacobs, David W.
通讯作者：
Jacobs, David W.
DOI：
10.1098/rspa.2007.1823
发表时间：
2007-05-08
影响因子：
3.5
作者：
Ballester, Pedro J.;Richards, W. Graham
通讯作者：
Richards, W. Graham