[Biojava-l] Isoelectric point and molecular weight calculations with BioJava

Peter Troshin p.v.troshin at dundee.ac.uk
Thu Feb 24 17:44:07 UTC 2011

Hi Andreas,

In fact I'd be happy to help with the development of the tools for 
simple physico-chemical properties calculation for peptides. We could 
port George’s code (assuming he is happy with this) from BioJava 1.8 but 
we can also provide a few other methods. A couple of projects in the lab 
where I work would have benefited from having these calculations readily 

I was thinking about participation in the Google Summer of Code (GoSC) 
this year as a mentor, and I think this would be an easy project for a 
student. What do you think about this?

Thank you for your prompt reply.


On 24/02/2011 16:54, Andreas Prlic wrote:
> Hi Peter,
> if you get a copy of biojava 1.8, it is still there. However I would
> like to port this to biojava 3 as well.. George do you want to help me
> with that, since you are one of the authors of this package? The basic
> support for chemistry in BioJava 3 is a bit better... (e.g. Element
> class)
> Andreas
> On Thu, Feb 24, 2011 at 7:33 AM, Peter Troshin<p.v.troshin at dundee.ac.uk>  wrote:
>> Hi,
>> I've noticed that BioJava up to about version 1.7 had an
>> org.biojava.bio.proteomics package, which had methods for isoelectric point
>> and molecular weight calculations for peptides. I could not find this
>> package in the BioJava 3.0.1 API. I’d like to use these methods and wonder
>> if there are any equivalent methods available in the latest version of
>> BioJava?
>> Thank you for your help,
>> Kind regards,
>> Peter
>> Dr Peter Troshin
>> Bioinformatics Software Developer
>> Phone: +44 (0)1382 388589
>> Fax: +44 (0)1382 385764
>> The Barton Group
>> College of Life Sciences
>> Medical Sciences Institute
>> University of Dundee
>> Dundee
>> DD1 5EH
>> UK
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