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

Question

[radha.jg]

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

Answer 1

[Asaf]

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

[radha.jg]

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

Answer 2

[Kevin Blighe]

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

[radha.jg]

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