![\"\"](\"/assets/images/prop_vs_commercial.png\")
Khanna and Ranganathan wrote up a review paper on molecular similarity (doi:10.1002/ddr.20404).\nI have not fully read it yet, but my eye fell on Table 1, which lists a number\nof programs that can be used to calculate QSAR descriptors, both open source\nand proprietary. However, the table features a column Availability which has\ntwo options: Public, Commercial. They qualify Bioclipse, CDK, and RDKit as public,\nand Dragon, MOE, CODESSA and others are commercial. Effectively, it seems to\nsuggest that they classify them as open source versus commercial, though I am\nnot entirely sure what they mean with public.
\n\nThe authors and referees would not be the first to make this common mistake:\nnot express the difference between two orthogonal axis: free-versus-commercial\nand open source-versus-proprietary. To clarify these axes, I created this diagram\n(CC-BY, SVG source\navailable upon request):
\n\n
It is very important to realize the Open Source software can be commercial.\nFor example, you can get commercial support for Bioclipse\nand CDK with GenettaSoft.\nIt is also really important to realize that free software (public?) does not\nmean it is Open Source (or visa versa). E-Dragon\nis an example here: you can freely use, but the source code is proprietary.\nSome years after open source cheminformatics took off, commercial providers\nstarted to provide free-for-academic-use packages, which fits into this category\ntoo.
\n\nReaders of my blog know that I advocate Open Source, not gratis software (see\nalso Re: Why I and you should avoid NC licences ),\neven though you can download many of the Open Source cheminformatics tools I\nworked on for free. Here it is important to realize that the CDK and Bioclipse\nare not free: it is just that the tax-payer covered the cost via academic institutes\nmostly, as well as hobbyists working out-of-office, like I have done for many,\nmany years, and companies who saw mutual benefit. Maybe something to consider\nthe next time you are wondering about donating money to an Open Source cheminformatics\nproject, and pay some respect to the project contributors of the software\nyou use.
\n\nOff-topic: there is a second inaccuracy in this table. For each software, they\nlist the number of descriptors, but without units. Units, units?? Yes. For\nexample, for the CDK they list “>40” descriptors, while for Dragon “3,224” (it\npuzzles me why you can count accurately above 3000, but not below 50. But the\npoint here is that the CDK count is really the number of Java classes, reflecting descriptor\nalgorithms. One algorithm can calculate more than one descriptor value, and\nthose are counted for Dragon. The columns is comparing apples with oranges.\nWhile I have never really counted it, and you every CDK user can in fact tune\nit, the number of calculated CDK descriptor values approaches a thousand. Well,\nI guess that is “>40” too :(
", "summary": "Khanna and Ranganathan wrote up a review paper on molecular similarity (doi:10.1002/ddr.20404). I have not fully read it yet, but my eye fell on Table 1, which lists a number of programs that can be used to calculate QSAR descriptors, both open source and proprietary. However, the table features a column Availability which has two options: Public, Commercial. They qualify Bioclipse, CDK, and RDKit as public, and Dragon, MOE, CODESSA and others are commercial. Effectively, it seems to suggest that they classify them as open source versus commercial, though I am not entirely sure what they mean with public.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/prop_vs_commercial.png", "date_published": "2010-12-21T00:00:00+00:00", "date_modified": "2026-10-17T00:00:00+00:00", "tags": ["cheminf","opensource"], "_references": [ { "url": "https://doi.org/10.1002/ddr.20404", "doi": "10.1002/ddr.20404" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }