[Bioperl-l] about pI prediction

[jun hu]

Hi, Everyone,
I use emboss pepstat and parse the result with some simple perl regular 
expression ... works fine... The problem is that the result is different 
from the results from expasy webserver, I guess they use different PKa 
values... Does anyone know where I can get a set of Pka values of all the 
amino acids, expecially those modified amino acids, like oxidated amino 
acid, phosphorylated amino acids, Itraq labeled lysine , etc,..., their pkas 
should be different from normal amino acids and the pIs from corresponding 
peptide will differ too.
Best,
Jun Hu
Bioinformatics Specialist
UMDNJ

>From: Conrad Halling <conrad.halling at bifx.org>
>To: Frank <lifei03 at gmail.com>
>CC: bioperl-l at portal.open-bio.org, Brian Osborne 
><brian_osborne at cognia.com>,   Marc Logghe <Marc.Logghe at devgen.com>
>Subject: Re: [Bioperl-l] about pI prediction
>Date: Wed, 18 May 2005 14:13:47 -0400
>
>Frank,
>
>The usual algorithm is to calculate the charge of the protein at a given 
>pH, say 7.0, then iterate to converge to a pH where the calculated charge 
>on the protein is zero.
>
>In BioPerl, the calculation is performed by sub _calculate_iep() in 
>Bio::Tools::pICalculator.
>
>For the latest stable release of EMBOSS, the code for calculating the pI is 
>in file EMBOSS-2.10/nucleus/embiep.c, function emblepPhConverge().
>
>For a more lucid explanation of how the algorithm works, see page two of 
>http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf.
>
>-- Conrad
>
>
>Frank wrote:
>>Hi, Thanks all, I wil install them and do some analysis.    I did it via 
>>net in http://us.expasy.org/tools/pi_tool.html before.  It is not so 
>>convenient for mass data analysis.
>>
>>Hi, Brian, do you have any idea about the principle of cacluate pI?  I 
>>searched some references published in 1980s. I am not sure whether it is 
>>out of date.
>>
>>Frank
>>
>>Brian Osborne wrote:
>>
>>>Frank,
>>>
>>>I've used both Tools/pICalculator and Tools/SeqStats.
>>>
>>>Brian O.
>>>
>>>-----Original Message-----
>>>From: bioperl-l-bounces at portal.open-bio.org
>>>[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Marc Logghe
>>>Sent: Tuesday, May 17, 2005 4:09 PM
>>>To: Frank; bioperl-l at portal.open-bio.org
>>>Subject: RE: [Bioperl-l] about pI prediction
>>>
>>>
>>>Hi Frank,
>>>
>>>
>>>>Dose anyone use the  bioperl module to predict pI and molecular weight 
>>>>of a protein?   Thanks
>>>>
>>>
>>>Don't know of a pure BioPerl module to predict pI. You can use
>>>Bio::Tools::SeqStats to get the molecular weight, though.
>>>If you have EMBOSS installed, you can use the Bioperl wrapper to the
>>>EMBOSS application 'pepstats' for both the pI and mol weight. Have a
>>>look at the docs for Bio::Factory::EMBOSS.
>>>However, you have to parse out the corresponding values. The EMBOSS
>>>docs, including an example output you can find at
>>>http://emboss.sourceforge.net/apps/pepstats.html
>>>HTH,
>>>Marc
>
>--
>Conrad Halling
>conrad.halling at bifx.org
>
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