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GLYCAM-L  November 2015

GLYCAM-L November 2015

Subject:

Re: Amber compactible heparin parameters

From:

Lachele Foley <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Sun, 22 Nov 2015 20:39:25 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (82 lines)

They are on the way. The student who developed them successfully
defended her thesis (Yay!) just recently. For that reason and several
others, you've caught us when we are a bit over-stressed. The
information should be available very soon. We will announce it here
and on the AMBER reflector.


On Sun, Nov 22, 2015 at 10:17 AM, anu chandra <[log in to unmask]> wrote:
> Hello Lachele,
>
> Thanks for prompt reply. I do understand the limitation of current naming
> convention in Glycam. It will be grateful, as you mention, if you can
> provide the prep file in 'Special release' section for 4DGlcpNSa1, which I
> can successively use for the heparin
> (LIdopA[2S]a1-4DGlcpNS[6S]a1-4LIdopA[2S]a1-4DGlcpNS[6S]a1-OH) I build on
> GAG-Builder.
>
>
> Many thanks
> Anu
>
> On Fri, Nov 20, 2015 at 6:10 AM, Lachele Foley <[log in to unmask]> wrote:
>>
>> It is correct for there to be no residue RYA in GLYCAM_06j-1.prep. To
>> use the name RYA makes logical sense, so I understand why it was
>> chosen, but it technically isn't the correct name to use.
>>
>> The current GLYCAM residue naming convention has numerous limitations,
>> and you have just encountered one. A new naming convention was
>> proposed in the article at the link just below. We want to switch to
>> this, or some other, more flexible naming convention, but doing so
>> will not be a trivial task and must be done with great care and
>> attention to detail.
>> http://glycob.oxfordjournals.org/content/18/6/426.full.pdf+html
>> (proposed new naming)
>>
>> So, Anu, I understand that your choice of the name RYA signifies the
>> fact that an SO3 is attached at positions 2 and 6, with another
>> monosaccharide at position 4. However, our naming doesn't recognize
>> an 'N' as an attachment position in that sense. The naming, at least
>> thus far, has only considered open valences at hydroxyl oxygens. So
>> there is no definition at all for attachments at "position 2" of a
>> GlcNAc or similar residue - note that there is also no residue called
>> '2YA' in the prep file.
>>
>> BTW, the RYA in Table 4 on our naming page (glycam.org/naming) is a
>> typo that has been present, but not noticed, since around the release
>> of GLYCAM-04.
>>
>> To other Woods/GLYCAM folks... We *could* adopt this naming, allowing
>> N to be an open valence. So, 2YA would be -2DGlcpNa1- with an open
>> valence at the N, which is at the 2 position. That might simplify
>> things in the meantime. We might not be able to generate all the
>> NAc-relevant residues in the database, but there would be names for
>> many of them. Also, this still doesn't give us a plain GlcpN, but we
>> don't have that anyway. It also might allow things to be attached
>> there that should not be. We could check to see if a lack of ff
>> parameters would keep this from being a problem in a simulation.
>>
>> Back to everyone: In the background, the builder currently calls the
>> files xYS for alpha and xYs for beta (for a lack of an official naming
>> convention). So, 4YS is -4DGlcpNSa1- and so forth. I can post those
>> prep files for now in the "Special Releases" section. I think that is
>> all Anu needs. We can always update the names and such later as
>> desired.
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>
>



--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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