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Question: Predict protein secondary structure from alignment
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gravatar for suzanne96yao
10 months ago by
suzanne96yao • 0
suzanne96yao • 0 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?
msa secondary structure alignment protein • 282 views
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modified 10 months ago by AsoInfo • 300 • written 10 months ago by suzanne96yao • 0

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

ADD REPLY • link written 10 months ago by jgreener • 260
0
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe ♦ 69k
Republic of Ireland
Kevin Blighe ♦ 69k wrote:

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

Kevin
ADD COMMENT • link written 10 months ago by Kevin Blighe ♦ 69k
0
gravatar for AsoInfo
10 months ago by
AsoInfo • 300
Bonn, Germany
AsoInfo • 300 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 COMMENT • link written 10 months ago by AsoInfo • 300
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