I did an in silico analysis for my protein to understand its secondary structure by using two servers; PSIPRED Workbench (http://bioinf.cs.ucl.ac.uk/psipred/) and SOPMA (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html). Both of them yield different results. Why does this happened?
Dear Fatin Safiudin ,
This can happen unfortunately. There are various reasons why:
-The accuracy of such programs is not 100% and most studies indicate percentages round 80% see for example https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-301
-The various prediction programs make use of different approaches, see the secondary structure section here https://en.wikipedia.org/wiki/Protein_structure_prediction#Secondary_structure
-The fact that related matters like the hydrophobicity depends on the hydrophobicity scale used, see also https://en.wikipedia.org/wiki/Hydrophobicity_scales
For a comparison and an idea of the spread (or similarities) you can find using different methods see for example Table 2 here:
Article The role and significance of potential lipid-binding regions...
See also my reply here https://www.researchgate.net/post/Which-online-tool-is-more-accurate-for-protein-secondary-structure-prediction with references towards some excellent papers.
Best regards.
Dear Fatin Safiudin
as Rob Keller told is something common since the realibility of prediction methods is not absolute.
Generally i'm performing this kind of prediction usingç
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_secco%20ns.html
which include different algoritms and on the basis of the agreement or not of the different predictions you can have an idea about the accuracy of the prediction on the different protein regions
ciao
Manuele
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