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<DIV dir=ltr align=left><SPAN class=351515317-18102012><FONT color=#0000ff
size=2 face=Arial>Let my try to clarify Arthur's comments regarding SEDNTERP.
SEDNTERP was written primarily for proteins/peptides. The current database does
<U>not</U> 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.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=351515317-18102012><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=351515317-18102012><FONT color=#0000ff
size=2 face=Arial>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.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=351515317-18102012><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=351515317-18102012><FONT color=#0000ff
size=2 face=Arial>Regarding the "<FONT color=#950f0b size=3
face="Times New Roman">unusual data file formats</FONT>" 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.</FONT></SPAN></DIV>
<DIV><SPAN class=351515317-18102012><FONT color=#0000ff size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=351515317-18102012><FONT color=#0000ff size=2
face=Arial>John</FONT></SPAN></DIV>
<DIV dir=ltr align=left><BR></DIV>
<DIV dir=ltr lang=en-us class=OutlookMessageHeader align=left>
<HR tabIndex=-1>
<FONT size=2 face=Tahoma><B>From:</B> rasmb-bounces@rasmb.bbri.org
[mailto:rasmb-bounces@rasmb.bbri.org] <B>On Behalf Of </B>Arthur
Rowe<BR><B>Sent:</B> Thursday, October 18, 2012 6:16 AM<BR><B>To:</B>
john_doran@vrtx.com<BR><B>Cc:</B> rasmb<BR><B>Subject:</B> Re: [RASMB] Is there
a facile method to get Vbar for smallmolecules without using
densitometry?<BR></FONT><BR></DIV>
<DIV></DIV><FONT class=Apple-style-span color=#950f0b>Dear John</FONT>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b>I guess that the most widely
used software for this purpose is SEDNTERP. It is now cross-platform, and there
is a web version:</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><A
href="http://www.spinanalytical.com/auc-software.php">http://www.spinanalytical.com/auc-software.php</A></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b>Only snag is that the current
versions call for rather unusual data file formats</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b>KInd regards</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b>Arthur</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b>Professor Arthur J
Rowe<BR>NCMH/Food Sciences<BR>University of Nottingham<BR>Sutton
Bonington<BR>Leics LE12 5RD UK<BR><BR>Tel: +44 115 9516156<BR><A
href="mailto:arthur.rowe@nottingham.ac.uk">arthur.rowe@nottingham.ac.uk</A></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#950f0b><BR></FONT></DIV>
<DIV><BR>
<DIV>
<DIV>On 17 Oct 2012, at 22:21, <A
href="mailto:john_doran@vrtx.com">john_doran@vrtx.com</A> wrote:</DIV><BR
class=Apple-interchange-newline>
<BLOCKQUOTE type="cite"><FONT size=2 face=sans-serif>Greetings fellow Rasmb
members</FONT><BR><BR><FONT size=2 face=sans-serif>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? </FONT><BR><BR><FONT size=2 face=sans-serif>Thank you
in advance for any replies that are sent to address this
problem!</FONT><BR><BR><BR><FONT size=2 face=sans-serif>John D Doran,
Ph.D.<BR>Protein Biochemistry<BR>Vertex Pharmaceuticals Inc.<BR>130 Waverly
Street<BR>Cambridge, MA
02139<BR>617-444-6142</FONT><BR>_______________________________________________<BR>RASMB
mailing list<BR><A
href="mailto:RASMB@rasmb.bbri.org">RASMB@rasmb.bbri.org</A><BR>http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb<BR></BLOCKQUOTE></DIV><BR>
<DIV>
<DIV><BR></DIV>
<DIV><BR></DIV><BR class=Apple-interchange-newline></DIV><BR></DIV><BR>
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