Background: Many molecules of interest are flexible and undergo significant shape deformationÃ‚Â as part of their function, but most existing methods of molecular shape comparison (MSC) treatÃ‚Â them as rigid bodies, which may lead to incorrect measure of the shape similarity of flexibleÃ‚Â molecules.
Results: To address the issue we introduce a new shape descriptor, called Inner Distance ShapeÃ‚Â Signature (IDSS), for describing the 3D shapes of flexible molecules. The inner distance is defined asÃ‚Â the length of the shortest path between landmark points within the molecular shape, and it reflectsÃ‚Â well the molecular structure and deformation without explicit decomposition. Our IDSS is storedÃ‚Â as a histogram which is a probability distribution of inner distances between all sample point pairsÃ‚Â on the molecular surface. We show that IDSS is insensitive to shape deformation of flexibleÃ‚Â molecules and more effective at capturing molecular structures than traditional shape descriptors.Ã‚Â Our approach reduces the 3D shape comparison problem of flexible molecules to the comparisonÃ‚Â of IDSS histograms.
Conclusion: The proposed algorithm is robust and does not require any prior knowledge of theÃ‚Â flexible regions. We demonstrate the effectiveness of IDSS within a molecular search engineÃ‚Â application for a benchmark containing abundant conformational changes of molecules. SuchÃ‚Â comparisons in several thousands per second can be carried out. The presented IDSS method canÃ‚Â be considered as an alternative and complementary tool for the existing methods for rigidÃ‚Â MSC. The binary executable program for Windows platform and database are available fromÃ‚Â https://engineering.purdue.edu/PRECISE/IDSS.
Link to paper:Ã‚Â Ã‚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:Ã‚Â 19463181.