I want to find method or web tools to calculate the pka and helicity of peptide，please help me，thanks！The length of my peptides is 9 and 19.
Dear Dong yu Chen ,
For your pKa (and isoelectric point) calculations there are numerous tools, I think one of the best is: IPC 2.0 https://ipc2.mimuw.edu.pl and the corresponding paper is Kozlowski, L. P. (2021). IPC 2.0: prediction of isoelectric point and pKa dissociation constants. Nucleic acids research, 49(W1), W285-W292.
There are numerous tools for peptide secondary prediction, see for example:
PEP-FOLD https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/
Jpred4 https://www.compbio.dundee.ac.uk/jpred/
PSIPRED http://bioinf.cs.ucl.ac.uk/psipred/
There are many more tools, see for a nice overview of the various methods: Kashani-Amin, E., Tabatabaei-Malazy, O., Sakhteman, A., Larijani, B., & Ebrahim-Habibi, A. (2019). A systematic review on popularity, application and characteristics of protein secondary structure prediction tools. Current drug discovery technologies, 16(2), 159-172. (see enclosed file)
Best regards.
Thank you very much! I calculated the pKa value of the peptide with IPC 2.0, but found "there are meaningless for the peptides (
Ah I see, not sure whether it is a remark made by the developers to be on the safe side while the results are in the end pretty good but have a look at the following paper where they claim to have used seven different methods/programs:
Chan, C. H., Wilbanks, C. C., Makhatadze, G. I., & Wong, K. B. (2012). Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PloS one, 7(1), e30296. Article Electrostatic Contribution of Surface Charge Residues to the...
Best regards.
Thank you very much! I will read this paper in detail, thanks for your help! Rob Keller
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