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\section{Methods}  We organize software packages into eight categories: cheminformatics, visualization,  QSAR (quantitative structure–activity relationship software), relationship) and ADMET modeling,  quantum chemistry, protein structure modeling, protein ligand  dynamics modeling, and free energy calculations,  virtual screening,de novo ligand design,  and visualization. ligand design.  We identified open-source open source  software package by browsing the relevant categories (Molecular Science, Chemistry, Bio-Informatics, Medical Science) on the popular SourceForge (\url{http://sourceforge.net}) repository, searching for categories on GitHub (\url{http://github.com}), searching for categories on OpenHub (\url{https://www.openhub.net}), searching for categories together with ``open-source ``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. For simplicity, BSD-like licenses (e.g. NCSA) are reported as BSD. 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 reported by Google Scholar, 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.