Chemoinformatics p0wned by cheminformatics... #2

Some time ago Noel ran a poll on chemoinformatics and cheminformatics, so I set up a poll too in part #1 of this series . The outcome is clear: less than 1 minute read

Jmol 11.6 RC 18 in Bioclipse

Just updated Bioclipse2 with Jmol 11.6 RC 18: less than 1 minute read

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. 6 minute read

Who likes my FriendFeed posts most...

Felix has a small tool on his website to show me (or anyone else) who likes what I post on my FriendFeed account: less than 1 minute read

JChemPaint history: CML patches in 1999

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint. Below is the email Christoph dug up from his archives: 1 minute read

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-pick which 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. less than 1 minute read

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. 1 minute read