pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides

The
isoelectric point of a peptide is a physicochemical property
that can be accurately predicted from the sequence of the peptide
when the peptide is built from natural amino acids. Peptides can however
have chemical modifications, such as phosphorylations, amidations,
and unnatural amino acids, which can result in erroneous predictions
if not accounted for. Here we report on an open source program, pICalculax,
which in an extensible way can handle pI calculations of modified
peptides. Tests on a database of modified peptides and experimentally
determined pI values show an improvement in pI predictions when taking
the modifications into account. The correlation coefficient improves
from 0.45 to 0.91, and the root-mean-square deviation likewise improves
from 3.3 to 0.9. The program is available at https://github.com/EBjerrum/pICalculax