Latest version 1.3.1 (Feb 25 2020)


ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.

The software has been ported to Linux, Mac OS X, and Microsoft Windows platforms.

Contact information

Mikko Vainio
email: mikko piste vainio at abo piste fi

Bibliographic reference

Mikko J. Vainio, J. Santeri Puranen and Mark S. Johnson (2009) ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. J. Chem. Inf. Model. 49, 492-502.
The structures used for the test runs are available for download.


Åbo Akademi University, Department of Biochemistry and Pharmacy, especially the folks at Structural Bioinformatics Laboratory.

Thanks to Susanna Repo, Jukka V. Lehtonen, and Mikko Huhtala for suggestions and inspiring discussions.

The development of ShaEP was made possible by funding from the Academy of Finland and Sigrid Jusélius Foundation.

Other software from our group

Balloon, a 2D to 3D structure conversion and conformational analysis program. Optionally assigns partial atomic charges to pre-generated conformers.

McQSAR, multi-conformational quantitative structure-activity relationships engine.