Overview of E3FP


The Extended 3-Dimensional FingerPrint (E3FP) 1 is a 3D molecular fingerprinting method inspired by Extended Connectivity FingerPrints (ECFP) 2, integrating tightly with the RDKit. It is developed by the Keiser Lab at UCSF and maintained primarily by Seth Axen.

For a thorough description of E3FP, please consult the original paper 1 and paper repository or Usage and Examples.

Documentation is hosted by ReadTheDocs.


Development occurs on GitHub. Contributions, feature requests, and bug reports are greatly appreciated. Please consult the issue tracker.


E3FP is released under the GNU Lesser General Public License version 3.0 (LGPLv3).

Briefly, this means E3FP can be used in any manner without modification, with proper attribution. However, if the source code is modified for an application, this modified source must also be released under LGPLv3 so that the community may benefit.

Citing E3FP

To cite E3FP, please reference the original paper 1.



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


Rogers D & Hahn M. Extended-connectivity fingerprints. J. Chem. Inf. Model. 50: 742-54 (2010). Access the paper