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

George Waldon gwaldon at geneinfinity.org
Thu Feb 24 19:15:06 UTC 2011

Hello Peter & Andreas

I effectively did some work on these methods, mostly fixing and adding  
the ExPASy algorithm that was kindly provided to me. I think it makes  
a lot of sense to port all physico-chemical property calculations  
related to amino acids and polypeptides to bj3, as suggested by  
Andreas, and I definitively support the effort. We could smoothly  
deprecate the bj1 package when this is done. Let me know how I could  


Quoting Peter Troshin <p.v.troshin at dundee.ac.uk>:

> 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 available.
> 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.
> Regards,
> Peter
> 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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