pIPredict Version 2: New Features and PTM Analysis

  • V.S. Skvortsov Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121, Russia
  • N. N. Alekseychuk Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121, Russia
  • Yu. V. Miroshnichenko Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • A. V. Rybina Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
Keywords: protein; peptide; isoelectric point; posttranslational modifications; property prediction

Abstract

pIPredict was created as a tool for prediction of the isoelectric point of peptides and proteins. It can also generate virtual 2D electrophoresis maps. The method of pI prediction is based on the Henderson-Hasselbach equation. In a new version the ProMoST and our new scales of pKa values were added. The other added features included: correction of electrophoretic shift by analyzing amino acid composition of proteins and prediction of pI values for proteins with a new set of posttranslational and other chemical modifications. Prediction of pI for proteins with PTM can be used to predict position of modified proteoforms on the virtual 2D electrophoresis map or as the tool of identifying which particular proteoform was observed in the experiment.The program also includes several widely used pKa scales, that can partially calculate values for proteins with some post-translational modifications. pIPredict is created as JAVA application and is freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.

References

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Published
2018-06-25
Section
Protocols of Experiments, Useful Models, Programs and Services