Background: Many molecules of interest are flexible and undergo significant shape deformationÂ as part of their function, but most existing methods of molecular shape comparison (MSC) treatÂ them as rigid bodies, which may lead to incorrect measure of the shape similarity of flexibleÂ molecules.
Results: To address the issue we introduce a new shape descriptor, called Inner Distance ShapeÂ Signature (IDSS), for describing the 3D shapes of flexible molecules. The inner distance is defined asÂ the length of the shortest path between landmark points within the molecular shape, and it reflectsÂ well the molecular structure and deformation without explicit decomposition. Our IDSS is storedÂ as a histogram which is a probability distribution of inner distances between all sample point pairsÂ on the molecular surface. We show that IDSS is insensitive to shape deformation of flexibleÂ molecules and more effective at capturing molecular structures than traditional shape descriptors.Â Our approach reduces the 3D shape comparison problem of flexible molecules to the comparisonÂ of IDSS histograms.
Conclusion: The proposed algorithm is robust and does not require any prior knowledge of theÂ flexible regions. We demonstrate the effectiveness of IDSS within a molecular search engineÂ application for a benchmark containing abundant conformational changes of molecules. SuchÂ comparisons in several thousands per second can be carried out. The presented IDSS method canÂ be considered as an alternative and complementary tool for the existing methods for rigidÂ MSC. The binary executable program for Windows platform and database are available fromÂ https://engineering.purdue.edu/PRECISE/IDSS.
Link to paper:Â Â http://www.biomedcentral.com/content/pdf/1471-2105-10-157.pdf
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Liu YS, Fang Y, Ramani K. IDSS: deformation invariant signatures for molecular shape comparison. BMC Bioinformatics. 2009 May 22;10:157. PMID:Â 19463181.