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

Wed Mar 2 05:12:19 UTC 2011

Hi Peter,

we still don;t know yet if we will have support from Google again this
year. Once we have a confirmation we will use the wiki site again for
hosting pages related to GSoC. However we should do this project in
any case...

Andreas

On Mon, Feb 28, 2011 at 7:18 AM, Peter Troshin <p.v.troshin at dundee.ac.uk> wrote:
>>>> What other functionality would you
>>>> like to see that is currently not there?
>
>
> I think that the methods below would be a good starting point, then the
> Google Summer of Code student can propose something else that he/she would
> fancy implementing.
>
>  Molecular weight
>  Extinction coefficient
>  Instability index
>  Aliphatic index
>  Grand Average of Hydropathy
>  Isoelectric point
>  Number of amino acids in the protein (His, Met, Cys)
>
> I know BioJava projects were managed under Open Bioinformatics Foundation
> (OBF) during last years GSoC. Is there a page for this year GSoC ideas
> somewhere?
>
> Regards,
> Peter
>
>
> On 25/02/2011 05:12, Andreas Prlic wrote:
>>
>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>>> 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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