how to get 3Dstructure of protein by ab-initio method

[Amara]

hello,

I have to predict 3D structure of protein. but any homolg of my
protein is not predicted , similarity is ver low, so i have to use ab-
initio method .. can anybody tell me some good tool of ab-initio
prediction instead of robetta and rosetta.
thank you

[chandan kumar]

u can get 3D structure of ur sequence on protein data bank

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chandan
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[Giovanni Marco Dall'Olio]

This is old, but still very useful:
- http://www.russell.embl-heidelberg.de/gtsp/flowchart2.html

You can probably get good result with just using Swiss-Model:
- http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1

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My blog on bioinformatics (now in English): http://bioinfoblog.it

[Wen Hwa Lee]

Amara -

have a quick search on the CASP website- there you will find the latest results by different groups/ methods:

http://predictioncenter.org/

Have a look at the latest round of fully published and analysed CASP results (CASP8):
http://www.predictioncenter.org/casp8/results.cgi

and then, flter the results by clicking on 'TM' (= 'Template Free Modelling' = ab-initio)

Then pick any of the cases and have a look at the most successful algorithms.


Giovanni - I am afraid that Swiss-Model doesn't do ab-initio modelling (only comparative modelling = homology modelling)

[miss_ss]

hi..
I also carry the ab initio analysis but still in the beginning.. maybe
you can try the I-TASSER server (http://zhang.bioinformatics.ku.edu/I-
TASSER/) as it is mentioned to be the best in recent CASP. However, I
would like to ask, if anyone here know the step by step way to carry
the ab initio?