Chem-bla-ics turns 3!

Five days ago, my chem-bla-ics blog turned 3. Here’s the first post . It defined: less than 1 minute read

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