3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison
aSchool of Software, Tsinghua University, Beijing, China
bKey Laboratory for Information System Security, Ministry of Education of China
cTsinghua National Laboratory for Information Science and Technology
dINRIA, Domaine de Voluceau-Rocquencourt, , 78153 Le Chesnay Cedex, France
eSchool of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
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.
Downloads:
Results:
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.
Conclusions:
The new software, named 3DMolNavi, has been developed for retrieval and navigation during flexible molecular shape comparison. 3DMolNavi is based on the IDSS histogram 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 CATH and MolMovDB. Compared to other shape descriptors, our tool achieves better 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.
Contact:
Dr. Yu-Shen Liu, Email address: liuyushen@tsinghua.edu.cn.
Meng Wang, Email address: wm0409@gmail.com.
Meng Wang, Email address: wm0409@gmail.com.