Using diffusion distances for flexible molecular shape comparison

BMC Bioinformatics

Research Article

Karthik Ramani¹  William Benjamin¹  Guo-Qin Zheng²  Qi Li²  Yu-Shen Liu³ 

[1] Purdue University, West Lafayette, IN, USA;School of Software, Tsinghua University, 100084, Beijing, China;School of Software, Tsinghua University, 100084, Beijing, China;Key Laboratory for Information System Security, Ministry of Education of China, Beijing, China;Tsinghua National Laboratory for Information Science and Technology, Beijing, China;

关键词: Diffusion Distance;    Topological Change;    Geodesic Distance;    Shape Descriptor;    Shape Deformation;   

DOI  :  10.1186/1471-2105-11-480

 received in 2009-11-04, accepted in 2010-09-24,  发布年份 2010

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Liu et al; licensee BioMed Central Ltd. 2010