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Secondary structure prediction correctness meassure

Dear everyone, various secondary structure predictors from amino acid sequences produce different results, that's ok, but is there any way (a meassure, or something) that can hint me which prediction is likely to be better than the others? Thank you :)

sequence secondary structure prediction
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updated by Erik Wright Erik Wright • written by henry slade henry slade

PSIPRED is the one that I used most. Is that the one you are using? I usually try to combine that result with conserved motifs (i.e. secondary helixes or sheets) should be more conserved.

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written by jiwpark00 jiwpark00

I'm using PSIRED, GOR and Spider2, then, is the reliability of the prediction rather a question of personal experiences?

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written by henry slade henry slade

1 answer

Typically there is an associated probability for the prediction at each position. For example, the GOR method provides probabilities for H, E, or C states. These can be calculated in R using the DECIPHER package:

library(DECIPHER)
aa <- AAStringSet("MALKNFNPITPSLRELVQVDKTNLWKGRP")
PredictHEC(aa, type="probabilities")

I hope that helps!

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written by Erik Wright Erik Wright

Hi I want to predict the secondary structure of amino acids of protein by retrieving it from PDB in R. How can I use PredictHEC? What could be the raw code for this purpose?

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written by 786 786

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