Latest version 1.8.2 (March 13 2022)


Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.

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 references

Mikko J. Vainio and Mark S. Johnson (2007) Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. Journal of Chemical Information and Modeling, 47, 2462 - 2474.
The structures used for the test runs are available for download.

J. Santeri Puranen, Mikko J. Vainio, and Mark S. Johnson (2010) Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. Journal of Computational Chemistry, 31, 1722 - 1732.


The development of Balloon v1.0.0 has been supported by Visipoint Ltd.

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

Thanks to Santeri Puranen, Susanna Repo, and Mikko Huhtala for suggestions and inspiring discussions.

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

Other software from our group

ShaEP performs rigid-body superimposition of 3D molecular models, such as those generated by Balloon.

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