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IsoelectricPointMetric

Author: Sharon Guffy (sharonguffy@gmail.com)

The IsoelectricPointMetric is used to predict the isoelectric point of a protein based on its sequence using one of several available algorithms. Note that this metric is not currently compatible with noncanonical amino acids or non-protein molecules. Available algorithms:

  • IPC_protein
    • Citation: Lukasz P. Kozlowski. IPC – Isoelectric Point Calculator. Biol Direct. 2016; 11: 55.
    • Website: http://isoelectric.org
    • Notes: Optimized for proteins. Benchmarks indicate that it outperforms most other algorithms including those available via IsoelectricPointMetric.
  • IPC_peptide
    • Citation: Lukasz P. Kozlowski. IPC – Isoelectric Point Calculator. Biol Direct. 2016; 11: 55.
    • Website: http://isoelectric.org
    • Notes: Optimized for small peptides.
  • Nozaki_Tanford
    • Citation: Nozaki Y, Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions: establishment of a hydrophobicity scale. J Biol Chem. 1971;246(7):2211–2217.
    • Notes: pKa values based on pKa of side chain groups in model compounds similar to the amino acids
  • Patrickios
    • Citation: Patrickios CS, Yamasaki EN. Polypeptide amino acid composition and isoelectric point. II. Comparison between experiment and theory. Anal Biochem. 1995;231(1):82–91. doi: 10.1006/abio.1995.1506.
    • Notes: Highly simplified model computed on small peptides. Not generally recommended for use on proteins.
  • Bjellqvist
    • Citation: B. Bjellqvist, G. J. Hughes, C. Pasquali, N. Paquet, F. Ravier, J. C. Sanchez, S. Frutiger, D. Hochstrasser, Electrophoresis 14 (1993) 1023–1031.
    • Website: https://web.expasy.org/compute_pi/, among others
    • Notes: One of the most commonly used set of pKa values for pI calculations.
  • EMBOSS
  • ProMoST
    • Citation: Halligan BD1, Ruotti V, Jin W, Laffoon S, Twigger SN, Dratz EA. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W638-44.
    • Website: http://proteomics.mcw.edu/promost.html
    • Notes: Uses a more complex algorithm that takes into account the identities of terminal residues for both terminus and side chain pKa values. Developed to determine effects of posttranslational modifications on pI--note that these modifications are not currently recognized by IsoelectricPointMetric.

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