eMolFrag Webserver

Assuming that organic compounds are composed of sets of core fragments (bricks) connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. Here, we developed eMolFrag, an automated method to extract molecular fragments from compound libraries. Chemical building blocks provided by eMolFrag can subsequently be used to construct virtual screening libraries for targeted drug discovery.
If you find eMolFrag useful, please cite the following paper:

eMolFrag is also available as a standalone software distribution. See the manual for instructions on how to use the webserver as well the details on the output file format.

eMolFrag is free of charge under the terms of GNU General Public License for non-commercial use. It is distributed without any warranty, but with best wishes.

This server is running eMolFrag 2017/01/18. Click here to see some sample results.


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3-10 alphanumerical characters.


Up to 1000 compounds in either MOL2 or SDF format.


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© Michal Brylinski
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