F@H & protein folding

[Sifu Sifulan]

Hie guys,

 

Currently I'm very intrested in protein folding simulations influenced by my computational chemistry lecture. We learned using Discovey Studio to predict the protein domains and folding. The software is too much expensive that only 10 PCs in my university installed with that software (obviously I can't afford to buy). In the internet there are many project and sotfware used for folding and docking simulations, I just don't know which one is user friendly and easy to access. I have try studied Folding@Home however my computer can't even download the program. Therefore I really hope somebody in here can show me the right path of protein folding simulation...

 

Thanks in advance!

[insane_alien]

i don't think folding@home will do what you want.

 

with F@H you don't get to choose what is folded, you get sent a work unit by the central server, your computer works through it and then sends the results back and gets another work unit.

[SL]

If you are just interested in the results and not in the actual process of protein folding, you might want to use external servers. Those are generally free of charge, but if you want to use them in class it might take a while to get the results (at least if all students request the results).

For modeling the 3D-structure of proteins using comparative modeling you could use SWISS-MODEL ( http://swissmodel.expasy.org/ ).

For secondary structure and transmembrane domain prediction alone, another tool to consider would be PSIPred ( http://bioinf.cs.ucl.ac.uk/psipred/psiform.html ).

If you prefer consensus prediction using several different algorithms, another website you could try @NPS ( http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_seccons.html ).

For viewing the structures I'd use RASMOL, it has all the basic functionality you need and also doesn't cost anything ( http://rasmol.org/ ).

[ivanp84]

You should try BioPuppy linux. It comes on single LiveCD (bootable) and it has collection of bioinformatics programs. Beside molecular visualization programs (RasMol, Garlic, ...), BioPuppy has secondary structure prediction tools and protein-ligand docking tools.

BioPuppy site: biopuppy.org

For molecular visualization I prefer JMol (has all RasMol capabilities plus much much more).

JMol@sourceforge: jmol.sourceforge.net

And, not to forget, JMol is Java program, so to run you first must install Java framework from Sun microsystems official site for yours platform (or you can try to find binary package for your gnu linux distribution). To run JMol jar archived try this from console: java -jar JMol.jar

The best way for analyzing secondary protein structure is with general purpose statistics software. I use R project for everyday statistics. (www.r-project.org)

In R you can perform very subtile multivariate tests (for example MANOVA analysis for significance in protein motifs, etc.) and graphical analysis, also R is programming language with S language superset.

Edited August 22, 2009 by ivanp84