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E3FP: Extended 3-Dimensional FingerPrint

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E3FP [1] is a 3D molecular fingerprinting method inspired by Extended Connectivity FingerPrints (ECFP) [2], integrating tightly with the RDKit.

Documentation is hosted by ReadTheDocs, and development occurs on GitHub.

Installation and Usage

For installation and usage instructions, see the documentation.

See the E3FP paper repository for an application of E3FP and all code used for the E3FP paper [1].


E3FP is available under the GNU Lesser General Public License version 3.0 (LGPLv3). See the documentation for more details.


[1](1, 2) Axen SD, Huang XP, Caceres EL, Gendelev L, Roth BL, Keiser MJ. A Simple Representation Of Three-Dimensional Molecular Structure. J. Med. Chem. 60 (17): 7393–7409 (2017). Access the paper Access the preprint on bioRxiv Access the recommendation on F1000Prime
[2]Rogers D & Hahn M. Extended-connectivity fingerprints. J. Chem. Inf. Model. 50: 742-54 (2010). Access the paper