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

Yu-Shen Liu123*, Meng Wang1, Jean-Claude Paul14 and Karthik Ramani5

Author affiliations

1 School of Software, Tsinghua University, Beijing 100084, China

2 Key Laboratory for Information System Security, Ministry of Education of China, Beijing 100084, China

3 Tsinghua National Laboratory for Information Science and Technology, , Beijing 100084, China

4 INRIA, Domaine de Voluceau-Rocquencourt, , 78153 Le Chesnay Cedex, France

5 School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA

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Citation and License

BMC Bioinformatics 2012, 13:95  doi:10.1186/1471-2105-13-95

Published: 14 May 2012



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 interaction. 3DMolNavi can be accessed via webcite.