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\section{Methods}  We organize software packages into eight categories: cheminformatics, QSAR (quantitative structure–activity relationship software), quantum chemistry, protein structure modeling, protein dynamics modeling, virtual screening, de novo ligand design, and visualization.  We identified open-source software package by browsing the relevant categories (Molecular Science, Chemistry, Bio-Informatics, Medical Science) on the popular SourceForge (\href{http://sourceforge.net}) (\url{http://sourceforge.net})  repository, searching for categories on GitHub (\href{http://github.com}), (\url{http://github.com}),  and searching for categories together with ``open-source software'' on Google. For every identified software package, we determine its license and assign it a qualitative activity score. Activity scores are assigned as follows:   \begin{enumerate}