Question: Can anyone reccomend me a software predictor of secondary structures from aminoacid sequence
0
gravatar for radha.jg
6 months ago by
radha.jg0
Uruguay
radha.jg0 wrote:

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

proteins sequence • 183 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe67k • written 6 months ago by radha.jg0
1
gravatar for Asaf
6 months ago by
Asaf8.4k
Israel
Asaf8.4k wrote:

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

ADD COMMENTlink written 6 months ago by Asaf8.4k

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

ADD REPLYlink written 6 months ago by radha.jg0
1
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

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

ADD COMMENTlink modified 6 months ago • written 6 months ago by Kevin Blighe67k

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

ADD REPLYlink written 6 months ago by radha.jg0
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