pIPredict: A computer tool for prediction of isoelectric points of peptides and proteins

  • V. S. SkvortsovEmail author
  • N. N. Alekseytchuk
  • D. V. Khudyakov
  • I. V. Romero Reyes


The data on approximate values of isoelectric point (pI) of peptides obtained during their fractionation by isoelectric focusing can be successfully used for the creation of the pKa scale for amino acid residues. This scale can be used for pI prediction for any peptide. Such the data of peptide fractionation also provide information about various post-translational modifications (PTMs), so that the pI values may be predicted for a wide range of protein forms. In this study, pKa values were calculated using a set of 13448 peptides (including 300 peptides with PTMs significant for pI calculation). The pKa constants were estimated for N-terminal, internal and C-terminal amino acid residues separately. The comparative analysis has shown that our scale increases the accuracy of pI prediction for peptides and proteins and successfully competes with tra- ditional scales and such methods as support vector machines and artificial neural networks. The prediction performed by this scale, can be made in our program pIPredict with GUI written in JAVA as an executable jar-archive. The program is freely available for academic users at The software has also the possibility of pI prediction by some other scales; it recognizes some PTMs and has the ability to use a custom scale.


peptide isoelectric point posttranslational modifications property prediction 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Giglione, C., Boularot, A., and Meinnel, T., Cell. Mol. Life Sci., 2004, vol. 61, pp. 1455–1474. doi:  10.1007/s00018-004-3466-8 CrossRefGoogle Scholar
  2. 2.
    Heller, M., Ye, M., Michel, P.E., Morier, P., Stalder, D., Jünger, M.A., et al., J. Proteome Res., 2005, vol. 4, no. 6, pp. 2273–2282. doi:  10.1021/pr050193v CrossRefGoogle Scholar
  3. 3.
    Po, H.N. and Senozan, N.M., J. Chem. Educat., 2001, vol. 78, pp. 1499–1503. doi:  10.1021/ed078p1499 CrossRefGoogle Scholar
  4. 4.
    Bjellqvist, B., Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S., and Hochstrasser, D.F., Electrophoresis, 1993, vol. 14, pp. 1023–1031. doi:  10.1002/elps.11501401163 CrossRefGoogle Scholar
  5. 5.
    Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., The Proteomics Protocols Handbook, 2005, pp. 571–6071. doi:  10.1385/1-59259-890-0:571 CrossRefGoogle Scholar
  6. 6.
    MELANIE version 7.0, GeneBio, Switzerland.Google Scholar
  7. 7.
    Patrickios, C.S., J. Colloid Interface Sci., 1995, vol. 175, pp. 256–256. doi:  10.1006/jcis.1995.1454 CrossRefGoogle Scholar
  8. 8.
    Perez-Riverol, Y., Audain, E., Millan, A., Ramos, Y., Sanchez, A., Vizcaíno, J. A., Wang, R., Muller, M., Machado, Y.J., Betancourt, L.H., Padrón, G., and Besada, V., J. Proteomics, 2012, vol. 75, pp. 2269–2274. doi:  10.1016/j.jprot.2012.01.029 CrossRefGoogle Scholar
  9. 9.
    Gauci, S., Van Breukelen, B., Lemeer, S.M., Krijgsveld, J., and Heck, A.J., Proteomics, 2008, vol. 8, pp. 4898–4906. doi:  10.1002/pmic.200800295 CrossRefGoogle Scholar
  10. 10.
    Romero Reyes, I.V., Fedyushkina, I.V., Skvortsov, V.S., and Filimonov, D.A., Int. J. Math. Model. Meth. Appl. Sci., 2013, vol. 7, pp. 303–310.Google Scholar
  11. 11.
    Romero Reyes, I.V., Otsenka affinnosti kompleksov belok-ligand s primeneniem neironnykh setei (Affinity Estimation for Protein-Ligand Complexes by Means of Neuronal Networks), Cand. Sci (Phys.-Math.) Dissertation, Moscow, 2014.Google Scholar
  12. 12.
    Chemaxon, Budapest, Hungary, Scholar
  13. 13.
    Pasquali, M., Serchi, T., Renaut, J., Hoffmann, L., and Bohn, T., Electrophoresis, 2013, vol. 34, pp. 505–509. doi:  10.1002/elps.201200256 CrossRefGoogle Scholar
  14. 14.
    Wong, P., Walter, M., Lee, W., Mannhaupt, G., Münsterkötter, M., Mewes, H.W., Adam, G., and Güldener, U., Nucleic Acids Research, 2011, vol. 39, Suppl. 1, pp. D637–D639. doi:  10.1093/nar/gkq1016 CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2015

Authors and Affiliations

  • V. S. Skvortsov
    • 1
    Email author
  • N. N. Alekseytchuk
    • 1
  • D. V. Khudyakov
    • 1
  • I. V. Romero Reyes
    • 1
  1. 1.Institute of Biomedical ChemistryMoscowRussia

Personalised recommendations