PDB 1ten protein folding

Film of a protein folding in poing, a new computational protein folding model. Note that the final conformation is not the real conformation for 1ten. See https://sourceforge.net/projects/poing/

The name for this model was inspired by Poing by Rotterdam Termination Source, http://www.youtube.com/watch?v=dqD1OohY2to

Category:

Film & Animation

Tags:

• protein
• science
• animation
• CGI

[empyrean101]

How do you render images from an atomic coordinate file? Raster3D, OpenGL?

[benlablondon]

I've written an opengl protein renderer, which is useful for watching the simulation as it proceeds.

[dhfrman]

r u able to use bluegene IBM'S protein folding program

[benlablondon]

I don't think IBM have their own protein folding software, they are working with academics to simulat proteins using molecular dynamics. This involves simulating all atoms, and interactions between them, very very slowly, to get as accurate a model as possible.

[benlablondon]

This may be the ultimate solution to the protein folding problem, however it is currently very slow (months!), can only be used to fold quite small proteins, and even then is sometimes quite inaccurate. The world's most powerful computers are used to perform molecular dynamics, as well as using distributed processing such as folding@home.

[benlablondon]

We aim to simulate the folding of smallish proteins (80-150 amino acids) in around an hour using a single desktop PC. Note that this is not to disrespect or underestimate the work of IBM, which I'm sure will be quite amazing!

[MrHarrytubing]

this is like porn for biological scientists :D

[benlablondon]

There is a good overview on Wikipedia (search for Protein structure prediction) of general methods for protein structure prediction and modelling. We're aiming to publish a paper on our method fairly soon, and I will post a link to it when that is out!

[TexasRounder]

I am very interested to learn more about what mathematical techniques you may know about that are being used to analyze this problem?

[benlablondon]

The software to simulate folding, and the software for making the video, were both developed by myself: together they are called poing. I hope to release this software in the near future under an open source license - pending a publication.