Posts Tagged Bioinformatics
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 Genetics” David 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!
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.
If anything, then it’s the MultipleSequenceAlignment (MSA) problem (in combination with the folding problem) which defines the core of bioinformatics. At least from my perspective, since that’s from where I started out my adventures in the field. Already fold.it successfully demonstrated for protein folding that it is possible to tackle hard problems by crowd-sourcing, a.k.a. Citizen Science. After all, the pattern recognition software installed on the wetware between your ears is highly evolved and can complement pure in-silico calculations. With Phylo researchers from McGill university have taken this approach to the sequence level:
Phylo is a challenging flash game in which every puzzle completed contributes to mapping diseases within human DNA.
Although the call for CitizenScience is not entirely new, it is boosted by such developments over the internet significantly. Who said that science and fun do not go together and can only be done while wearing a labcoat and operating extremely expensive machinery (?) – quite the opposite!
Biochemist Erwin Chargaff advocated a return to science by nature-loving amateurs in the tradition of Descartes, Newton, Leibniz, Buffon, and Darwin — science dominated by “amateurship instead of money-biased technical bureaucrats”.
Now that’s some company to be proud of. And I can’t say I completely disagree, albeit I’d like to think the two are not necessarily mutually exclusive (for-the-love-of-it vs. for-profit). If you’d like to get started, check out the tutorial video below and have fun aligning!
Reference: “Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment” by Alexander Kawrykow, Gary Roumanis, Alfred Kam, Daniel Kwak, Clarence Leung, Chu Wu, Eleyine Zarour, Phylo players, Luis Sarmenta, Mathieu Blanchette and Jérôme Waldispühl (2012) PLoS ONE 7(3): e31362. doi:10.1371/journal.pone.0031362
“HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment” by Michael Remmert, Andreas Biegert, Andreas Hauser & Johannes Söding (Nature Methods 9, 173–175 (2012) doi:10.1038/nmeth.1818)
“HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.”
The entire suite of programs is available for all major OSs.
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 VizBi-2012 Conference took place in Heidelberg this week – unfortunately I couldn’t attend it. Nevertheless, I received a bit of summary and feedback: The talks will be made available online, I am looking forward to check out a few of them (i.e. Jim Robinson, Jernej Ule). Ivet Bahar (ProDy) and Valerie Daggett (Dynameomics) gave an interesting overview on Molecular Dynamics.
Thanks to to Corinna Vehlow for feedback!