Using diffusion distances for flexible molecular shape comparison

Background: Many 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. Results: In 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. Concl...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Yu-Shen Liu, Qi Li, Guo-Qin Zheng, Karthik Ramani, William Benjamin
• Keywords: BMCBI 2010, Diffusion Distances, Molecular, Shape Descriptors