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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}), searching for categories together with ``open-source software'' on Google, and browsing the Click2Drug (\url{http://click2drug.org}) and VLS3D \cite{Villoutreix_2013} directories. For every identified software package, we report its primary URL and software license and assign it an activity code. Activity codes consist of a development activity level (alphabetical) and usage activity level (numerical). In cases where download statistics are not available/applicable usage is subjectively ranked based on external references to the tool (e.g., message list posts, source code forks, citations, etc.). In cases were a package does not follow an open development model (i.e., source is only released with official releases) the estimate of development activity will be overly conservative.