3D Modelling of Proteins and DNA

Judging from the gallery and videos, the Graphite – LifeExplorer is a great tool to model protein and DNA :

The Graphite-LifeExplorer modeling tool to build 3D molecular assemblies of proteins and DNA from Protein Database (PDB) files. Atomic DNA can be modeled from scratch or reconstructed from simulation.

Unfortunately, I didn’t get the Mac-Version to work on my machine (Mac OS X 10.6.8) it works only for OS X 10.7.+ (got it running on 10.7.3) – it’s definitely worth keeping an eye on:

shared by Damien Larivière via LinkedIn/Molecular Modeling in Life Sciences.

Biophilia

Biophilia is an extraordinary and innovative multimedia exploration of music, nature and technology by the musician Björk. Comprising a suite of original music and interactive, educational artworks and musical artifacts, Biophilia is released as ten in-app experiences that are accessed as you fly through a three-dimensional galaxy

I still haven’t downloaded and checked out the app myself in detail, the price-tag is a bit hefty for my taste. So far I have never spend over 10 bucks on a single app, and personally find it very hard to digest more than 2 Björk-songs in a row. OK, my ears aren’t bleeding, and in this case my eyes are very much tempted by the visuals. Biophilia contains several subsections (in-apps), so one could argue it’s more than just a single app, comparable to an entire (concept?-)album. On the app-store reviews there’s some criticism of the pricing-policy, however content-wise one reviewer goes as far as claiming that “we will eventually see Biophilia as the Sergeant Peppers of music apps“. A steep claim indeed to liken it to the fab four… but even though the music is not exactly my cup of tea, I am thrilled by the unique combination of contemporary art, science and technology.

As for the scientific content, the spring 2012 issue of the quarterly newsletter published by the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB for short) features a snapshot of the video for Björk’s title “hollow”:

To accompany the song “Hollow,” Björk’s meditation on biological ancestry, [Biomedical animator Drew] Berry
created a lush landscape for DNA to replicate (and sparkle) to the music. Molecular
machines work at real-time speed, culminating in the appearance of Björk as a complex
protein structure. Many of the molecular shapes, illustrated with great depth and rich
color, were created with the help of crystal structure data from the PDB.

More of these stunning, educational and award-winning 3D animations by Drew Berry and his colleagues are available on WEHI.TV at the Walter+Elisabeth Hall Institute of Medical Research. Enjoy!

so many Molly-Cules

Just a couple of days ago the PDB hit over 80.000 structures – that’s a lot of structural information at the molecular level to go by, especially since the 40k mark was surpassed just 5 years ago. That also means that we get now the same number of new entries every year as were available in total around 1998.

In this context, I came across this Directory of computer-aided Drug Design tools at the Swiss Institute for Bioinformatics (SIB, see flowchart of the DrugDesign-pipeline below).

I also came across this list of software and resources at the National Center for Dynamic Interactome Research (NCDIR).

And finally, on the topic of drug-design, there is “the saga of Molly” – Although there is commercial interest behind the blog (no problem there for the critically yet open-minded reader), I like the tale because it is written from an entirely different perspective, and, as you know, I like looking at things from a different angle.

This is the tale of one molecule’s long sojourn from the organic lab through Phase III clinical testing.  Be forewarned – it’s written from the understandably limited and skewed perspective of the molecule.

(molecular) Happy New Year !

The PSI Structural Biology Knowledgebase released their annual Calendar. Similar to “the Cal” by Pirelli, the 2012 issue is featuring tantalizing renderings of some of the finest models around.

… a very sophisticated concept of beauty, mid-way between fashion and glamour. And every year the Cal offers a collection of images that interpret the concept of beauty in an original way, different to the previous year.

In some (aeehh, broad sense, admittedly) this applies to the PDB version as well, I guess it’s a a must have for the structural biologist! The .PDF file is available here, the card on the right is from the corresponding RCSB PDB News.

Happy Holidays!

OMG (OhMightyGraph)! This year is almost over, so I’d like to thank you, my dear reader, for your kind interest. WordPress reports well over 3200 clicks for “cistronic”, which has now been up here for about a year. The rendering of the nucleosome (PDB:1KX5) in the style of a bubbly xmas candle wrapped in green DNA is meant as a virtual seasons greeting card from yours truly, courtesy of the organisation in the core of your cells.

I’ll be travelling a couple of days and hence updates and new posts will probably occur quite infrequently until January. But with more than 120 posts in total now there is plenty to dig through! In the meantime, if you’d like to make my day, take a couple of minutes for a brief comment or email: What’s your (most/least) favourite post, which topics deserve more depth and coverage, what’s missing? Any hints, criticism, praise, questions and interesting additions are very much welcome.

I wish you a happy and healthy 2012, stay curious and tuned for more to come. Cheers!

ATP Synthase movie

The proton driven turbine cranking out ATP – beautifully animated.
More background info at http://www.mrc-mbu.cam.ac.uk/research/atp-synthase.

shared by Rajini Rao via google+.

New Modeller release – 9.10

Modeller – One of the best approaches to structure prediction – just got an overhaul:

(Modeller) 9.10 is primarily a bugfix release relative to the last public release
(9.9). Major user-visible changes include:

• Add Python 3 support
• Add support for Mac OS X 10.7 (Lion)
• Modeller on 64-bit Macs is now built with Intel Fortran, resulting in a roughly 2x speedup compared to 9.9.
• Add Unicode support; all filenames should be UTF-8 encoded.

See the Modeller manual for a full change log: http://salilab.org/modeller/9.10/manual/node38.html

by email from Ben Webb, Modeller Caretaker (modeller-care@salilab.org)