I am looking for a tool which can predict Protein's structural class alpha, beta, alpha/beta, or other. from sequence. I need a standalone package. I tried looking up on internet, many of them are obsolete and are not supported. kindly give me list of standalone packages for this job.
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Edit - I note that you requested 'standalone', but it's possible to automate the process that I outline below, with creative programming skills.
If you start from any amino acid sequence, you can predict the protein conformation using the Protein Model Portal. These tools will generate a PDB file and email it to you (or you can download it from a link). Also see the posting here: A: pathogenicity predictors of cancer mutations
You can then view the PDB file in Jmol, and view various things such as hydrogen bonds, van der Waal's force at various levels, and di-sulphide bonds, and indeed α-helices and β-sheets.
Thanks, I am looking to run the program for around 10K proteins. Protein's structural class alpha, beta, alpha/beta. This approach may not be readily deployed.
You just have the amino acid sequence?; from a novel organism? One of the easiest things to automate would be a Protein BLAST, which would help to infer functionality of the sequences that you've got. Otherwise, I can assure you that the process above is 'automatable'.
While that may be true using the portal for 10K automated jobs may not be acceptable to Protein Model portal and may get var121.trading IP banned.
Great point - would additionally take a very long time, i.e., just not practical.
See if something from this list would work: http://www.sbg.bio.ic.ac.uk/people/rob/CCP11BBS/foldrec.html or https://en.wikipedia.org/wiki/Threading_(protein_sequence)#Protein_threading_software
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You can use one of the 2D structure prediction tools from EMBOSS.
Thanks, I am looking to run the program to predict Protein's structural class alpha, beta, alpha/beta. and not secondary structure of individual amino acids in the protein.