Right now, I am using ProtParam to compute GRAVY index of peptides. However, some of my peptides are post-translationally modified, and contains unusual amino acids. I assume that ProtParam does not incorporate these information to compute for the actual GRAVY index of my peptide.
Dear Simon Miguel Lopez ,
Interesting question. Indeed, ProtParam focussed on ‘conventional’ amino acids, see for reference: https://web.expasy.org/protscale/pscale/Hphob.Doolittle.html The GRAVY index for ‘unusual’ amino acids.
As far as I can see only one group made an attempt to come up with a more comprehensive hydrophobicity scale:
Tossi, A., Sandri, L., & Giangaspero, A. (2003). New consensus hydrophobicity scale extended to non-proteinogenic amino acids. In 27th European Peptide Symposium (pp. 416-417). Edizioni Ziino.
Unfortunately, I could not find a downloadable/accessible version of this interesting paper. As far as I can judge one could use the following site/server (however I tried it and it didn’t seem to work):
http://www.bbcm.univ.trieste.it/~tossi/HydroCalc/HydroMCalc.html
Not sure how active he is here onn RG but the researcher behind this research is Dr. Alessandro Tossi, you might try to contact him: https://www.researchgate.net/profile/Alessandro_Tossi
Do keep in mind that every hydrophobicity scale (including the Kyte-Doolittle scale used for GRAVY index calculations) are having its limitations, see for example:
Peters, C., & Elofsson, A. (2014). Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins: Structure, Function, and Bioinformatics, 82(9), 2190-2198.
Hope this answers your question somewhat.
Best regards.
Dear Simon Miguel Lopez ,
Interesting question. Indeed, ProtParam focussed on ‘conventional’ amino acids, see for reference: https://web.expasy.org/protscale/pscale/Hphob.Doolittle.html The GRAVY index for ‘unusual’ amino acids.
As far as I can see only one group made an attempt to come up with a more comprehensive hydrophobicity scale:
Tossi, A., Sandri, L., & Giangaspero, A. (2003). New consensus hydrophobicity scale extended to non-proteinogenic amino acids. In 27th European Peptide Symposium (pp. 416-417). Edizioni Ziino.
Unfortunately, I could not find a downloadable/accessible version of this interesting paper. As far as I can judge one could use the following site/server (however I tried it and it didn’t seem to work):
http://www.bbcm.univ.trieste.it/~tossi/HydroCalc/HydroMCalc.html
Not sure how active he is here onn RG but the researcher behind this research is Dr. Alessandro Tossi, you might try to contact him: https://www.researchgate.net/profile/Alessandro_Tossi
Do keep in mind that every hydrophobicity scale (including the Kyte-Doolittle scale used for GRAVY index calculations) are having its limitations, see for example:
Peters, C., & Elofsson, A. (2014). Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins: Structure, Function, and Bioinformatics, 82(9), 2190-2198.
Hope this answers your question somewhat.
Best regards.
Also check https://www.researchgate.net/profile/Seied_Mehdi_Miri/post/Could_you_recommend_any_detailed_reference_books_or_papers_introducing_how_to_use_proteomics-associated_databases_and_then_to_analysise_results/attachment/5a747af94cde266d5888466f/AS%3A589600397479936%401517583097483/download/Mass+Spectrometry+Data+Analysis+in+Proteomics.pdf
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