May 27, 2016

IPC - Isoelectric Point Calculator

BioRxiv : the Preprint Server for Biology
Lukasz P Kozlowski

Abstract

Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is critical for many biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Here, I present the Isoelectric Point Calculator, a web service for the estimation of pI using different sets of dissociation constant (pKa) values, including two new, computationally optimized pKa sets. According to the presented benchmarks, IPC outperform previous algorithms by at least 14.9% for proteins and 0.9% for peptides (on average, 22.1% and 59.6%, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Peptide and protein datasets used in the study and the precalculated pI for the PDB, SwissProt and some of the most frequently used proteomes are available for large-scale analysis and future development. The IPC can be accessed at http://isoelectric.ovh.org/.

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Mentioned in this Paper

Study
Polyacrylamide Gels
HIV Protease Inhibitors
Fingers
Mass Spectrometry
Proteomics
Proteome
4-dichlorobenzene
Isoelectric Focusing
Entire Capillary Blood Vessel (Organ)

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