I believe most commercial protein sequence analysis packages contain
a program to predict isoelectric points. If you have a Sun and
Sun's C++ compiler, there is a freely available program called iso
which is part of my molbio++ package (available via ftp from
golgi.harvard.edu).
Keep in mind that any isoelectric point estimation tends to ignore
post-translational modification, and many post-translational modifications
in eukaryotes involve derivatizing charged amino acid side chains or the
N-terminus as well as adding moieties which are themselves charged.
This is a particularly important consideration with extracellular &
cell surface proteins. The SwissProt entry for a protein generally
describes in detail the known post-translational modifications.
Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at biosun.harvard.edu
P.S. If someone is preparing a FAQ list, this Q would be a good addition
