How To Apply Chou-Fasman Parameter In A Protein Sequence?

Question

[Mkl]

Hi ,

I would like to find the Probability of alpha helix, beta sheet and turn from an amino acid sequence using chou- fasman parameter. I don't know whether it is possible in Biopython or in R. Any suggestions please.

Chou-Fasman formula is CFs(X)= (ns(X)/N(X))/(ns/N).

Any books or journals for reference will be appreciated.

Answer 1

[Neilfws]

The Chou-Fasman method is simple, but a little more involved than your formula: see this page for the details.

Since it uses a simple algorithm, it's quite easy to implement in any programming language. In R, the seqinr package (PDF) contains data which includes the Chou-Fasman parameters. For Python, see this tutorial page.

There are also sure to be "ready-made" solutions (scripts, software) which implement Chou-Fasman and other secondary structure prediction algorithms - see e.g. the EMBOSS suite.

[Mkl]

@neilfws. I couldn't find chou-fasman related function in seqinr package. Could you tell me the name of the function? or any other packages available for this in R? Can I do this in Biopython? I think, that will be easy than python.

[Neilfws]

There isn't a function, but data(aaindex) includes the Chou-Fasman parameters. That's a good starting point to write your own function. At present, I don't know of a ready-made solution in either R or Biopython.