Abstract

Background

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.

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 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 https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html webcite.

Comments

This is the publisher pdf of Yu-Shen Liu, Meng Wang, Jean-Claude Paul, Karthik Ramani. 3DMolNavi: A Web-Based Retrieval and Navigation Tool for Flexible Molecular Shape Comparison. BMC Bioinformatics 2012, 13:95 (14 May 2012) and is available at: 10.1186/1471-2105-13-95.

Date of this Version

5-14-2012

DOI

10.1186/1471-2105-13-95

Download

Share

COinS