pIPredict: A computer tool for prediction of isoelectric points of peptides and proteins
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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 http://www.ibmc.msk.ru/LPCIT/pIPredict. 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.
Keywordspeptide isoelectric point posttranslational modifications property prediction
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