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

[Andreas Prlic]

Great, seems we have an agreement that we want to improve
functionality for this. How complex is this going to be? From quickly
checking the 1.8 source it looks like just a few classes that need to
be converted and not too painful.  What other functionality would you
like to see that is currently not there?

Andreas


On Thu, Feb 24, 2011 at 8:08 PM, Scooter Willis <willishf at ufl.edu> wrote:
> We put in some basics regarding modeling amino acid properties in the
> core module but really didn't have any pressing use cases to drive the
> api beyond calculating the mass of a peptide. We currently have
> getMolecularWeight() as a method in AbstractCompound but never added a
> getSequenceMolecularWeight() to AbstractSequence. It would be great to
> get the attributes/features of amino acids properly modeled in core
> and extend when reasonable useful summary methods at higher levels.
> You should be able to query mass of a peptide and have it valid for an
> amino acid with a PTM which means the amino acid needs to support the
> ability to be modified in a flexible manner. I spent the last year+
> developing a software suite for peptide detection in MS data for
> deuterium exchange where automated PTM detection was important. Would
> be great to get some focused attention on the core to make sure we can
> model nucleotides and amino acids with a chemistry friendly API.
>
> Thanks
>
> Scooter
>
> On Thu, Feb 24, 2011 at 2:15 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
>> 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 help.
>>
>> Thanks
>> George
>>
>> 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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>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>
>>>
>>>
>>
>>
>>
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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