Fourth in the CDK Literature series. Really, a follow up on #3 which I\nwanted to get out, even though not really finished yet. But, after 3 comes 4, not 3b. Maybe 3.1, but that suggests at least 3.2-3.9 too,\nlet alone full R (that was supposed to the space of all reals…) I’ll stick to positive non-zero integers.\n#1 and\n#2 are still available too.
\n\nAnother thing I should remark is that this series does not provide full reviews of the cited papers. Instead, it provides a list of papers\nthat cite one of the two CDK papers (doi:10.1021/ci025584y and\ndoi:10.2174/138161206777585274). It is worth repeating that these two articles are not the\nonly article which describe CDK source code, and maybe I should start listing papers that cite other articles that discuss CDK source\ncode. Anyway, the other papers discussing CDK source code are listed in an\noverview I maintain in the CDK wiki (now on\nSourceForge), but have not updated it for #4 and #3 yet.
\n\nPunnaivanam Sankar and Gnanasekaran Aghila published a paper where they propose a knowledge framework for mechanisms of organic reactions,\nand used an XML framework combined with a ontology for the semantics. JChemPaint and the CDK are cited as opensource tools that support\nreactions.
\nPunnaivanam Sankar, Gnanasekaran Aghila, Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML\nMarkup Procedures, J. Chem. Inf. Model., 2007, 47(5):1747 -1762, doi:10.1021/ci700043u
Ma et al. have published a (Chinese) QSAR paper where CDK descriptors have been as molecular represention of a data set with 212 ligands\nfor the P-glycoprotein. Models have been build with Random Forests, and classification\nsuccess rates for the test set of around 85%.
\nGuang-Li Ma, Xiao-Ping Zhao, Yi-Yu Cheng, Identification of P-gp substrates using a random forest method based on chemistry development\nkit descriptors, Chemical J. of Chinese Universities-Chinese, 2007, 28(10):1885-1888
sMOL is GPL-licensed software for setting up a small molecule database.\nThe software uses JChemPaint, OpenBabel, JOELib and the CDK for\nchemoinformatics functionality, and R and Weka for statistical analyses. I have not locally installed it yet, but the\nUser Guide shows really nice screenshots. The\nInstaller Guide shows a quite polished product too.\nNot sure how open the project is to contributions from others (patches, translations, etc, but will ask.
\nSupawadee Ingsriswang, Eakasit Pacharawongsakda, sMOL Explorer: an open source, web-enabled database and exploration tool for Small\nMOLecules datasets, Bioinformatics, 2007, 23(18):2498-2500, doi:10.1093/bioinformatics/btm363
Bruno Villoutreix wrote an overview of free (as in free beer) services to aid virtual screening. It cites the CDK, Jmol, OpenBabel as\ntools, along with a long list of free but proprietary tools. It does explicitly plead for opensource docking and scoring tools, and,\nas such, potentially useful in grant proposals.
\nBruno Villoutreix, Nicolas Renault, David Lagorce, Olivier Sperandio, Matthieu Montes, Maria Miteva, Free Resources to Assist\nStructure-Based Virtual Ligand Screening Experiments, Current Protein and Peptide Science, 2007, 8(4):381-411,\ndoi:10.2174/138920307781369391
Fangping Mu et al. have set up a KEGG-derived database with annotated reactions where atoms between\nreactants and products are mapped, to help data analysis of isotopomeromics data. The CDK rendering features are used for\nvisualization purposes. The software also builds on\nBioMeta, work by Martin Ott ,\npresented at last years CDK Workshop.
\nFangping Mu, Robert Williams, Clifford Unkefer, Pat Unkefer, James Faeder, William Hlavacek, Carbon-fate maps for metabolic reactions,\nBioinformatics, 2007, 23(23):3193-3199, doi:10.1093/bioinformatics/btm498
I got two more papers lined up, but do not have access to Current Pharmaceutical Design.
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