Protein structure

A Most Ugly Hack: translating from CHARMM to AMBER trajectories

Ever wondered how you might translate trajectories from one Molecular Dynamics package to another? It's a thorny little problem that's afflicted quite a few structural biologists. Here's one ugly solution that I am rather proud of.


Practical BioGrids

Recycle or Globus Toolkit?
If you're the kind of bioinformatician who is interested in using Grid or Web Services, then the Practical High Throughput Computing for Bioinformatics course held at Imperial College London, on the 16th to 20th July, would probably be worth attending.


A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions

One of the most spectacular flameouts in science happened last year. In a short letter (barely over 300 words long) published in Science in the very last issue of 2006, Geoffrey Chang, a crystallographer, retracted 3 Science articles, a Nature article, a PNAS article and a JMB article. The sum of 5 years of work was destroyed, apparently, over a single sign error in a data-processing program. Read more...


ComBio 2006

It's been 3 years since I made it to a meeting - that was ISMB 2003, here in Brisbane. Next week I'll be attending ComBio2006...here in Brisbane. Ah well.

The "com" in ComBio is "combined" rather than "computational" - it's a large conference for a number of Australian/New Zealand life science societies. There are 10 streams including several of interest to Nodalpointers, especially bioinformatics/systems biology, gene expression/regulation and protein structure/function. I'll do my best to blog any interesting stuff here and at my place, possibly "live" depending on the facilities.

update: the blogging is at my place and it ain't live thanks to the (non) facilities.


announcement: Geneious - freeware bioinformatics data analysis and visualization tool

This is an announcement of a bioinformatics tool, published as freeware for the community.

Geneious is an easy-to-use, cross-platform (Windows, OS X, Unix) bioinformatics data analysis and visualization tool. It has an open API for writing plugins. You can use Geneious to compare genes from different species, to build an evolutionary tree to see how closely related they are, or to search for literature on any topic in medicine or biology. You can view and extract gene annotations from whole genomes, and interactive 3D graphics allow you to move around protein structures.

Version 1.0 of Geneious has just been published as freeware. Biomatters hopes that you will put the program to good use in your research, and we are eager to hear your comments and feedback.


WHY DO PROTIENS HAVE UNWANTED RESIDUES IN THEIR SEQUENCE?

Isoenzymes have similar function but different
structures.

             
This means these protiens have similar active sites. We know that some enzymes
even if their polypeptide chain is shortened can perform their function.
So what's the Use of these "unwanted" amino acids?
                             
Please make me Knowledgable in this scientific query.


hi

hi
i m new to this blog.hope we share informations that benefits all.
three cheers to bioinformatics


Survey Question

Hello, I'm about to start a survey/literature review on "Protein Sequence Classification" or something of the sort. I was wondering if anyone has any advice on what tools I should be using. Particularly anything to keep track of all the references? searching for references? and what program to write it in?

Any and all comments are welcome


Associate Director - Sr Project Manager - Neuro studies

Where are you research scientists to be found for hire? Particularly around Palo Alto? Need 5 of you. Recruiter.


What can computers do for biologists?

When I gave one of my first talks at my current workplace on Perl, BLAST and genomic analysis, a nameless audience member asked me a question I have never forgotten. "It strikes me that what you're doing is rather desperate", she said, "wouldn't you be better off doing some experiments?"

At the time, I was rendered almost speechless (there is no polite way to answer such a question), but I've since learned that many biologists (at least at my current workplace...) are not aware of the paradigm shift brought about by computational biology. Namely, rather than stumble about choosing research topics and experiments almost at random, you can make intelligent use of information (i.e. process it computationally) and use that as a way to direct and focus your research.

The folks at the UGA CSB Lab seem to understand that, so next time you're faced with such a question, direct your questioner to something like this Powerpoint (sorry) slide.


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