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

[Peter Troshin]

>>>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
>>>>>>
>>>>>>
>>>>>>
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>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>>
>>>>
>>>
>>>
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