R-omes aren’t build in a day

where R ∈ {Prote, Interact, Gen, …}

Tommy Carstensen

[…] built a model of DNA out of LEGO bricks (of PDB entry 2DAU, to be precise) to celebrate the 40th anniversary of the PDB. The clip also has educational value, explaining some of the basics of DNA structure and more.

[posted by Gerard J. Kleywegt via pdb-l mailing list (pdb-l@sdsc.edu)] For all those which are under the jurisdiction (=curse?) of the GEMA: the video (mp4) can also be found here.

Thanks Tommy! I already feared the art of building models would be totally lost, so I am really happy to see this. Structural models, especially physical ones, are very central to the understanding and progress of molecular biology. It’s important not to get discouraged by those guys who hide their inability to think beyond a single dimension (sequence) behind a smug attitude towards our “toys” – they didn’t get the point. I’m convinced we won’t be able to make sense out of the high-throughput data without understanding the underlying structures and interactions, no matter how many petabytes of sequencing data are being accumulated. Don’t get me wrong: sequencing delivers important data, but it’s just part of the picture.

This is an opportunity to point out the pioneering work that has been done in establishing the PDB as a central resource for structural data. A nice account of the history and lessons to be learned for the current open science movement and open linked data efforts is “The PDB wasn’t built in a day: lessons in data sharing” by Maria Hodges on her blog “Wood for the trees“. See also her entertaining and insightful post on “How to build a bad biological database“.

Many disciplines are struggling with how to store and organize data, but we can all learn from the slow and steady progress of the PDB.

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  1. #1 by cistronic on 2011/12/27 - 11:53

further hints, constructive criticism, questions, praise

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