Clathrin is a three-legged protein complex or triskelion that can assemble into lattice-like structures. Inside the cell, this assembly helps to create vesicles: tiny packages of membranes containing proteins and goodies for the cell to use. Incredibly our first view of assembled clathrin was made in the 1960s, with resolution improving steadily since then. The image below shows these improvements.

Europe PMC has added protein and chemical structures from Protein Data Bank (PDB) and ChEBI via the BioEntities tab.

One of the many great pleasures of SciFoo was to meet with people who had a different, and in many cases much more comprehensive, view of managing data and making it available.

I am too tired to write anything even vaguely coherent. As will have been obvious there was little opportunity for microblogging, I managed to take no video at all, and not even any pictures. It was non-stop, at a level of intensity that I have very rarely encountered anywhere before.

Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2). But here it is. Day 3 Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit.

Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information.

While I was working on implementing proper author-given chain IDs in PDB structures for Jmol’s mmCIF reader today, I thought it was interesting to mention the recent article Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors by Nabuurs (DOI:10.1371/journal.pcbi.0020009, open access), working at the CMBI, two floors away from my former working location at the Radboud University Nijmegen.