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pKa prediction, or, how to convert a JCIM paper into Java
Lee et al. published last week a paper on pKa prediction (doi:10.1021/ci8001815). As the paper says, the pKa, and in particular the ionic state of a molecule at physiological pH, affects pharmacokinetics and pharmacodynamics. The paper describes a (binary) decision tree using presence or absence of SMARTS substructures to traverse the tree, allowing prediction of monoprotic molecules.
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Cherry-picking commits from CDK trunk: how to make a reasonable commit message
Some of you heard me complain about commit messages resulting from
git cherry-pickwhich allows me to apply patches from CDK trunk to a branch, without needing to do a full merge of what happens in trunk. The commit messages would be identical, which made it seem that those original messages were mine. -
Git mirror for the CDK
While slowly merging with Sweden, and ADSL which should reach my house in some two weeks, I am enjoying my new office space and Git to upload patches to the CDK. Christoph wondered if we should switch CDK from SVN to Git. A few developers objected, for various reasons: no native Windows clients (though msysgit might be the solution), no (stable) plugins for Eclipse, IDEA(?), etc.
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Moved to Sweden: Post-doc in the Bioclipse group of Prof. Jarl Wikberg
The reason why I have not been able to blog much lately, is that my family and I have been moving to Uppsala/Sweden, where I’ll start a postdoc in the group of Jarl Wikberg @ BMC @ Uppsala University, where I’ll work on chemoinformatics in drug design, and the use of CDK and Bioclipse in particular.
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FriendFeed for the Chemistry Development Kit
FriendFeed is a nice aggregation service allowing discussion of items posted from delicious, blogs, and any other RSS-based feed (e.g. my feed). It also has a room concept, where people can post stuff around a topic, such as a conference such as Science Blogging 2008 London, or the CDK:
