3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison.

BMC Bioinformatics
Yu-Shen LiuKarthik Ramani

Abstract

Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison treat them as rigid shapes, which may lead to incorrect measure of the shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible molecular shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible molecular shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of Macromolecular Movements (MolMovDB) and CATH. Compared to other shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible molecular shape comparison and enhance navigation for user's interact...Continue Reading

References

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Jan 23, 2009·BMC Bioinformatics·Yu-Shen LiuKarthik Ramani
May 26, 2009·BMC Bioinformatics·Yu-Shen LiuKarthik Ramani
Sep 28, 2010·BMC Bioinformatics·Yu-Shen LiuWilliam Benjamin

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Citations

Apr 4, 2014·BMC Bioinformatics·Hsin-Wei WangTun-Wen Pai
Aug 10, 2018·Frontiers in Chemistry·Ashutosh Kumar, Kam Y J Zhang

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Methods Mentioned

BETA
MDS

Software Mentioned

MolMovDB
Matlab
Flex
3D
3DMolNavi
Flash
SURFER
Mozilla Firefox
IDSS
Chrome

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