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Can anyone reccomend me a software predictor of secondary structures from aminoacid sequence

Hello all I have a multifasta with the protein sequences of an organism and I want to obtain a tsble of predictions of secondary structures similar to the output of TMHMM (http://www.cbs.dtu.dk/services/TMHMM/). The problem with TMHMM is that it only predicts alpha-helixes because it assumes all the proteins are transmembrane and doesn't consider beta-sheets.

So, can somebody reccomendme another software that can do the same thing but considering my requirements.

Cheers

Jenifer

sequence proteins
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updated by Kevin Blighe Kevin Blighe • written by radha.jg • radha.jg

2 answers

Good old PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/

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written by Asaf Asaf

Thanks for the recommendation. I'll check what it can do

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written by radha.jg • radha.jg

There used to be an interface at the Protein Model Portal that could allow one to easily use other modeling services; however, Protein Model Portal appears to no longer have funding.

I believe SWISS-MODEL is another option.

Also, ExPASy lists many other tools.

Kevin

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written by Kevin Blighe Kevin Blighe

Does SWISS-MODEL accept a non aligned multifasta, or just a sequence per upload?

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written by radha.jg • radha.jg

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