3DMolNavi Homepage


3DMolNavi is a web-based visualized navigation system developed for intuitively exploring flexible molecular shape retrieval. This system is based on the histogram of Inner Distance Shape Signature (IDSS)[1,2]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.

How to use it

Click here(Database set up in 12/20/2011, last updated in 2/28/2012) to start 3DMolNavi. Follow the instruction to automatically install Flash Player 10.2 and Java Runtime Environment if you have not installed them before.
If it is not properly displayed, you can also manually install Flash Player and Java Runtime Environment.
Already tested in Firefox 7,Chrome 14 and Internet Explorer 8, other browsers and versions may work well, but are not recommended.




1. Query a molecule like this: Enter "12e8-H" for the H chain of a molecule whose PDB ID is 12e8.

2. In the right, you can navigate the retrieved results in 3D space, you can also control totally with your mouse (click and use mouse wheel). More specific options can be used in the control panel.

3. The 3D shape of a molecule is shown on the left, and it accepts interaction and different display modes (right click), where Jmol is used for displaying. The IDSS of a molecule is also displayed on the left.

4. On the bottom-right, you can see the most relevant six molecules that are similar to a query molecule.

Demo image


[1] Yu-Shen Liu, Karthik Ramani, Min Liu. Computing the inner distances of volumetric models for articulated shape description with a visibility graph. IEEE Transactions on Pattern Analysis and Machine Intelligence(PAMI),2011,23(12):2538-2544.
Paper website: https://engineering.purdue.edu/PRECISE/VMID
[2] Yu-Shen Liu, Yi Fang, Karthik Ramani. IDSS: deformation invariant signatures for molecular shape comparison, BMC Bioinformatics, 2009, 10:157.
Paper website: https://engineering.purdue.edu/PRECISE/IDSS


Yu-Shen Liu(liuyushen@tsinghua.edu.cn)
Meng Wang(wm0409@gmail.com)