IPC - Isoelectric Point Calculator

ABSTRACT Accurate estimation of the isoelectric point ( pI ) based on the amino acid sequence can be useful 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 PDB, SwissProt databases are available for large-scale analysis and future development. The IPC can be accessed at http://isoelectric.ovh.org .