Question: Secondary structure prediction correctness meassure
1
gravatar for ldpubsec
2.8 years ago by
ldpubsec90
European Union
ldpubsec90 wrote:

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 :)

ADD COMMENTlink modified 2.8 years ago by Erik Wright360 • written 2.8 years ago by ldpubsec90

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.

ADD REPLYlink written 2.8 years ago by jiwpark00200

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

ADD REPLYlink written 2.8 years ago by ldpubsec90
3
gravatar for Erik Wright
2.8 years ago by
Erik Wright360
Erik Wright360 wrote:

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!

ADD COMMENTlink modified 2.2 years ago • written 2.8 years ago by Erik Wright360

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?

ADD REPLYlink written 4 weeks ago by 78650
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