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Handling data sets of small molecules in various file formats is day to day routine task. You may trust a script or other black-box approach 90% of the time, but every now and then you certainly want to see what's going on. Mona is an interactive tool that can be used to prepare and visualize small-molecule datasets.


Mona has been built on top of the well-known Naomi[1] cheminformatics framework that has been proven to be robust, accurate and extremely efficient. Mona facilitates:

  • Loading molecules files stored in SDF, MOL2 or SMILES-format
  • Scanning entire directories for molecule data
  • 2D depiction of hundreds of thousands of molecules
  • Duplicate removal
  • Filtering based on physic-chemical properties, functional groups, and substructures
  • SMARTSediting and SMARTSmatch-visualization
  • Set-operations such as union, intersection, sub-set splitting
  • Visualization of property distributions

For the benefit of interactive use, Mona has been equipped with a database backend that allows for an extremely efficient handling. Upon import numerous physic-chemical properties are calculated and deposited in the database. For a million molecules this may take half an hour. However, once stored you may close and re-open the database within a matter of a minute or two, gaining instant access to all properties and high-quality 2D depictions.
We recommend you to read the original publication[2].


take a look at the Mona tutorial movie


Mona may be used free of charge for academic research or evaluation purposes.
It is available for Windows 64bit, Linux and MacOS. Note that with the download you accept our terms and conditions*.

Download Mona for your operating system:
Linux 32bit Linux 64bit Windows 64bit Mac OS X

Since Mona will not run without a valid license, go ahead with one the following options:

* Terms and conditions:
Mona is a prototype developed by our academic partner at the Center for Bioinformatics (ZBH) of the University of Hamburg.
No support is granted any warranty or liability is hereby expressly excluded. You use Mona at your own risk!
Any publication in reference to Mona must cite the original publication[2].
[1]Urbaczek S., Kolodzik A., Fischer J.R., Lippert T., Heuser S., Schulz-Gasch T., and Rarey M.
NAOMI - On the almost trivial task of reading molecules from different file formats.
J. Chem. Inf. Model., 2011, 51 (12), pp 3199-3207
[2]Hilbig M, Urbaczek S., Groth I., Heuser S. and Rarey M.
Mona - Interactive Manipulation of Molecule Collections.
J. Chem. Inf., 2013, 5:38 doi:10.1186/1758-2946-5-38


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