Package Bio :: Package SeqUtils :: Module IsoelectricPoint
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Module IsoelectricPoint

source code

Calculate isoelectric points of polypeptides using methods of Bjellqvist.

pK values and the methos are taken from:

* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F.
The focusing positions of polypeptides in immobilized pH gradients can be
predicted from their amino acid sequences. Electrophoresis 1993, 14,

* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
Reference points for comparisons of two-dimensional maps of proteins from
different human cell types defined in a pH scale where isoelectric points
correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539.

I designed the algorithm according to a note by David L. Tabb, available at:

Classes [hide private]
A class for calculating the IEP or charge at given pH of a protein.
Variables [hide private]
  positive_pKs = {'H': 5.98, 'K': 10.0, 'Nterm': 7.5, 'R': 12.0}
  negative_pKs = {'C': 9.0, 'Cterm': 3.55, 'D': 4.05, 'E': 4.45,...
  pKcterminal = {'D': 4.55, 'E': 4.75}
  pKnterminal = {'A': 7.59, 'E': 7.7, 'M': 7.0, 'P': 8.36, 'S': ...
  charged_aas = ('K', 'R', 'H', 'D', 'E', 'C', 'Y')
  __package__ = None
Variables Details [hide private]


{'C': 9.0, 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'Y': 10.0}


{'A': 7.59,
 'E': 7.7,
 'M': 7.0,
 'P': 8.36,
 'S': 6.93,
 'T': 6.82,
 'V': 7.44}