moblog uk

Spidermonkey's Sporadic Lab Stuff

by Spidermonkey

user profile | dashboard

« older newer »

Hello World from the lab!

Part spider - part lab monkey, will do science for cash, strawberries, or for a place to be that's out of the rain (but preferably for cash).

The rest of what I get up to goes into the Tunnel of Goats :)

Urgent Science Stuff:

Please help reform English libel law
Current UK libel laws are very bad for science and free speech.

Cool science stuff:

RCSB Protein data bank: Molecule of the Month in alphabetical order

The PCR Song It's the little things that keep you going...

NCBI's Entrez Gene My favourite starting point for finding out what is known about any gene of interest.

NCBI's PubMed Where to go to find pretty much all research published in the last 30 years or so (may go back a lot further now). All newly published research is quickly added to the site.

The Genetic Code - table of the DNA/RNA triplet codes for amino acids. This is how DNA codes for protein.

Another PCR song Disco frenzy :)

Recent visitors

late night modelling session

(viewed 440 times)
Bookmark and Share
Thanks to
13th Nov 2009, 07:22  


Caine says:


15th Nov 2009, 22:05

Spidermonkey says:

I'm fairly new to all this protein modelling/protein-ligand interaction modelling stuff but it is pretty cool what you can do with freeware. Just opening the proteins up, and spinning them round in 3D, colouring in in different ways... My mind is quite boggled but, I hope, in a good way.

PHYRE is cool though. It's not perfect for every protein but you just paste in an amino acid sequence and it goes away and aligns it to any structures it can find that have similarity and gives you back the 3D structure it is most likely to occupy. Which is a good place to start.

16th Nov 2009, 03:29

Caine says:

I've seen some other 3D modeling, and it's fascinating. I think it's often helpful to see such stuff in 3D, at least for laymen who have to shove the brain into 5th gear to grok the science. ;)

16th Nov 2009, 03:49

Spidermonkey says:

3D is really helpful for everyone. The hardest bit is trying to convey to others what you have just seen rotating on the screen in 3D using 2D snapshots and words. I wave my hands a lot at this point like I'm holding an imaginary ball while people stare at me blankly.

16th Nov 2009, 03:54

Caine says:

Hahahaha. Perhaps you should invest in some cheap styrofoam balls from a craft store.

16th Nov 2009, 03:58

Spidermonkey says:

It has crossed my mind. I would need 246 amino acids for 1 and 251 for the other, but they would need to be different colours/shapes and connect in different ways to build it... If I did it at the atom scale (most useful for exploring interactions) I would need 4000 or so.

Could probably render the helices, loops and beta sheets/folds in pipe cleaners though!

16th Nov 2009, 04:21