Posts Tagged Protein
As a bioinformatician, I cannot help but point out that ComputerScience and stem-cell research are sharing such a prestigious award. Somewhat a confirmation of the idea that combining the two in a fruitful way is a very good idea, indeed. And in this context I’d like to mention Hans Schöler, whom I had the pleasure to listen to recently. In his excellent work he demonstrated that Oct4 plays a key-role in reprogramming. The structural underpinnings he presented were simply brilliant – see the PDB molecule-of-the-month article on “Oct and Sox Transcription Factors” as a substitute.
Utopia is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services.
The installation package (provided by the AdvancedInterfacesGroup AIG) includes
- CINEMA – multiple sequence alignment editor
- Ambrosia – molecular structure viewer
- UTOPIA – support libraries and plugins
After a quick & painless installation, it seems to work out of the box. More in-depth info when I get to grips with more of the functionality.
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.
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 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!
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.
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.
The International Molecular Exchange Consortium IMEx is the latest effort of data-providers to integrate Protein-Interaction Data –
- A non-redundant set of protein-protein interaction data from a broad taxonomic range of organisms
- the data in standards compliant download formats (MITAB or PSI-MI XML 2.5)
- Expertly curated from direct submissions or peer-reviewed journals to a consistent high standard.[ … aiming to … ]
- Develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals
- Make these interaction available in a single search interface on a common website
- Make all IMEx records freely accessible under the Creative Commons Attribution License
If you’ve been looking for that one-stop shop for getting a representative dataset of Protein-Protein Interactions, this just looks like it. There is an overview available on youtube (see below)
… and a training course on “Networks and Pathways Bioinformatics for Biologists” will take place at EMBL-EBI in May.
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.