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

[John Philo]

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



On 17 Oct 2012, at 22:21, 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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