Archive for category Molecules

The great ideas of biology

The guardian has a series called “It’s a small world“, among which is a video called “Gregor Mendel and the genesis of genetics” where

Nobel laureate Sir Paul Nurse tells the story of another great idea in biology – genes as the basis of heredity – in a lecture at the Royal Institution in London. It all started with the gardening monk Gregor Mendel and his peas in the 19th century and reached a key milestone with the unravelling of the molecule of heredity, the DNA double helix, by James Watson and Francis Crick in 1953

The great ideas of biology covered are

  • the cell
  • the gene
  • natural selection
  • Life as chemistry
  • Biology as an organized system.

Similarly to “A Brief Introduction to GeneticsDavid Murawsky (as mentioned around here before, but hey, they repeat stuff on TV all the time, and not only the goodies) put another impressive clip out there: “18 Things You Should Know About Genetics“. Enjoy!

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Nobel Prize in Technology

The 2012 Millennium Technology Prize (Technology Academy Finland) will be awarded to Linus Torvalds and Dr Shinya Yamanaka.

Linus Torvalds initiated LINUX about 20 years ago (as mentioned previously, see here).


Dr. Yamanaka pioneered work on induced pluripotent stem cells (iPS cells or iPSCs), using a combination of c-MycKlf4Oct-3/4, and Sox2.

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.

(found via heise.de and zdnet.com)

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Bioinformatics Utopia


While checking out the new InterPRO (in beta stage) I came across the latest version of Utopia (available for all major OSs) :

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.

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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.

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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!

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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.

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(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.

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