[RASMB] Is there a facile method to get Vbar for smallmolecules without using densitometry?

[Tom Laue]

Hi-
We still create the files for the web version, which must store some 
data locally.
Best wishes,
Tom
On 10/18/2012 2:40 PM, John Philo wrote:
> Let my try to clarify Arthur's comments regarding SEDNTERP. SEDNTERP 
> was written primarily for proteins/peptides. The current database does 
> _not_ incorporate the data from those Durschlag papers that allows you 
> to build up small molecules from individual atoms and groups of atoms, 
> and thus SEDNTERP cannot be used for John Doran's purpose.
> It would in principle be possible to add all those small molecule 
> building blocks as "conjugates" in SEDNTERP and then use them to build 
> up small molecules to calculate their vbar, and doing so would 
> probably be a good idea. But creating all those new database entries 
> would be a lot of work. If we have a volunteer, perhaps Tom Laue's 
> group can find a way to distribute those new entries and add them to 
> existing databases. I am not aware of any public domain utility that 
> does these small molecule vbar calculations.
> Regarding the "unusual data file formats" comment, I think Arthur is 
> referring to SEDNTERP's ability to write out or read in sample 
> compositions (amino acids and/or conjugates) as text files with a 
> ".smp" extension. It is never really necessary to create such 
> files---the full composition information is stored in the database 
> when you create a "sample" record. In all these years I've never ever 
> had a question about these files, and I doubt anyone ever uses them. 
> Thus frankly I'm surprised Tom Laue's group at UNH bothered to 
> implement that in version 2. Pretty much the only possible use for 
> these files would be as a means of transferring sample composition 
> information from one copy of a SEDNTERP experimental database to 
> another. As I recall the file format is simply two columns of text 
> with the name of the component and the number of moles so I'm not 
> clear why that is so unusual.
> John
>
> ------------------------------------------------------------------------
> *From:* rasmb-bounces at rasmb.bbri.org 
> [mailto:rasmb-bounces at rasmb.bbri.org] *On Behalf Of *Arthur Rowe
> *Sent:* Thursday, October 18, 2012 6:16 AM
> *To:* john_doran at vrtx.com
> *Cc:* rasmb
> *Subject:* Re: [RASMB] Is there a facile method to get Vbar for 
> smallmolecules without using densitometry?
>
> Dear John
>
> I guess that the most widely used software for this purpose is 
> SEDNTERP. It is now cross-platform, and there is a web version:
>
> http://www.spinanalytical.com/auc-software.php
>
> Only snag is that the current versions call for rather unusual data 
> file formats
>
> KInd regards
>
> Arthur
>
> Professor Arthur J Rowe
> NCMH/Food Sciences
> University of Nottingham
> Sutton Bonington
> Leics LE12 5RD UK
>
> Tel: +44 115 9516156
> arthur.rowe at nottingham.ac.uk <mailto:arthur.rowe at nottingham.ac.uk>
>
>
> On 17 Oct 2012, at 22:21, john_doran at vrtx.com 
> <mailto:john_doran at vrtx.com> wrote:
>
>> Greetings fellow Rasmb members
>>
>> The issue has arisen on more than one occasion for us to look at the 
>> association state of small molecules ( i.e molecules under 1000 MW) 
>> using the AUC. When there is plenty of material it is easy enough to 
>> directly measure Vbar using densitometry, but of course there are 
>> also occasions where the material is precious and there is not nearly 
>> enough for densitometry. Does anyone know of any alternative physical 
>> methods or getting Vbar values generated from theory that may be used 
>> in lieu of densitometry?
>>
>> Thank you in advance for any replies that are sent to address this 
>> problem!
>>
>>
>> John D Doran, Ph.D.
>> Protein Biochemistry
>> Vertex Pharmaceuticals Inc.
>> 130 Waverly Street
>> Cambridge, MA 02139
>> 617-444-6142
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>
>
>
>
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-- 
Department of Biochemistry and Molecular Biology
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