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. 2015 Jan-Feb;61(1):83-91.
doi: 10.18097/pbmc20156101083.

[pIPredict: a computer tool for predicting isoelectric points of peptides and proteins]

[Article in Russian]
V S Skvortsov, N N Alekseychuk, D V Khudyakov, I V Romero Reyes

[pIPredict: a computer tool for predicting isoelectric points of peptides and proteins]

[Article in Russian]
V S Skvortsov et al. Biomed Khim. 2015 Jan-Feb.

Abstract
in English, Russian

The data on approximate values of isoelectric point (pI) of peptides obtained during their fractionation by isoelectric focusing can be successfully used for the calculation of the pKa's scale for amino acid residues. This scale can be used for pI prediction. The data of peptide fractionation also provides information about various posttranslational modifications (PTM), so that the prediction of pI may be performed 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 calculated 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 traditional 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 executable jar-archive. The program is freely available for academic users at http://www.ibmc.msk.ru/LPCIT/pIPredict. The software has also the possibility of pI predicting by some other scales; it recognizes some PTM and has the ability to use a custom scale.

Dannye o priblizitel'nom znachenii pI, poluchennye v khode fraktsionirovaniia peptidov metodom izoélektricheskogo fokusirovaniia, mogut byt' s uspekhom ispol'zovany dlia rascheta shkaly znacheniĭ pKa aminokislotnykh ostatkov, na osnovanii kotoroĭ mozhno predskazat' pI dlia liubogo proizvol'nogo peptida. Takogo roda dannye soderzhat informatsiiu o razlichnykh posttransliatsionnykh modifikatsiiakh (PTM), blagodaria chemu predskazaniia pI mogut byt' osushchestvleny dlia shirokogo spektra belkovykh form. V nastoiashcheĭ rabote raschet shkaly znacheniĭ pKa proveden na osnovanii vyborki v 13448 peptidov, 300 iz kotorykh imeli PTM znachimye dlia rascheta pI. Konstanty dlia N-kontsevykh i C-kontsevykh aminokislotnykh ostatkov uchityvalis' samostoiatel'no. Sravnitel'nyĭ analiz pokazyvaet, chto ispol'zovanie nasheĭ shkaly povyshaet tochnost' predskazaniia pI kak dlia peptidov, tak i dlia belkov, s uspekhom konkuriruia kak s traditsionnymi shkalami, tak i s uzkospetsializirovannymi metodami predskazaniia, takimi kak metody opornykh vektorov i iskusstvennykh neĭronnykh seteĭ. Ispol'zovat' dannuiu shkalu dlia predskazaniia pI mozhno s pomoshch'iu razrabotannoĭ nami programmy s graficheskim interfeĭsom, napisannoĭ na iazyke JAVA v vide ispolniaemogo jar-arkhiva. Programma svobodna dlia ispol'zovaniia akademicheskimi pol'zovateliami i dostupna po adresu http://www.ibmc.msk.ru/LPCIT/pIPredict. V programme realizovany takzhe vozmozhnosti predskazaniia po riadu drugikh shiroko rasprostranennykh shkal, ucheta nekotorykh PTM i dobavleniia sobstvennykh variantov shkaly.

Keywords: isoelectric point; peptide; posttranslational modifications; property prediction.

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