Question: Predict protein secondary structure from alignment
0
gravatar for suzanne96yao
12 weeks ago by
suzanne96yao0 wrote:

Dear all,

I want to predict the secondary structure using MSA as input.

I looked up Jpred4, which can use both sequence fasta or alignment in fasta format as input. However, it only provides a RESTful API for users to submit the jobs to their server, and I would like to work locally instead.

PSIPRED is another option, but it seems to not accept B in the amino acid code...

Do you have any other recommendation?

ADD COMMENTlink modified 12 weeks ago by AsoInfo300 • written 12 weeks ago by suzanne96yao0

Does B mean either aspartic acid or asparagine? If so, you could replace B with D or N and run through PSIPRED.

ADD REPLYlink written 12 weeks ago by jgreener240
0
gravatar for Kevin Blighe
12 weeks ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

You may try one or more of the tools at the Protein Model Portal

Kevin

ADD COMMENTlink written 12 weeks ago by Kevin Blighe60k
0
gravatar for AsoInfo
12 weeks ago by
AsoInfo300
Bonn, Germany
AsoInfo300 wrote:

You can use JPred and also you can find the list of protein secondary structure prediction tools: https://molbiol-tools.ca/Protein_secondary_structure.htm

ADD COMMENTlink written 12 weeks ago by AsoInfo300
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