Re: [modeller_usage] How to incorporate NAD and water in my model

["Schmid, Dr R." <>]

Hi Charlie,

In the alignment file have you tried sth like the construct below?

>P1;template
<SNIP>
YIK/.* 

>P1;target
<SNIP>
HIK/.*

Make sure your residue selection includes your NAD
ie
structureX:template:1:A:4:A:.:.:.:.
for the example given would correspond to the pdb file template.pdb with
TYR 1 A, ... FAD 4 A  

Cheers,
Ralf

============================================
Dr Ralf Schmid
Lecturer in Bioinformatics
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road
Leicester  LE1 9HN  UK

Tel. +44 (0)116 229 7023
============================================
 


> -----Original Message-----
> From:  
> [">mailto:] On Behalf Of 
> Charlie Allerston
> Sent: 15 March 2007 16:22
> To: 
> Cc: 
> Subject: Re: [modeller_usage] How to incorporate NAD and 
> water in my model
> 
> 
> >Charlie Allerston wrote:
> >>Do you have to use the modeller alignment script?  I have 
> been using 
> >>ebi software to create a .pir file.
> >
> >No, you do not need to use Modeller to make your alignment file. 
> >However, since there are no standard one-letter codes for 
> ligands, you 
> >will likely have to edit your original alignment in a text editor to 
> >put in the ligands.
> >
> 
> This is what I am not getting.  Where to put the ligand in 
> the alignment, regardless of what character to use.
> Take this for instance.  trying to model something from the 
> template 1VDC http://www.rcsb.org/pdb/explore.do?structureId=1VDC
> Looking at the PDB file it has 316 residues then it had a 
> molecule of FAD tacked on at a position designated 400.
> So when I align this to some target like below (cropped).
> 
> 
> --------------------------MNGLETHNTRLCIVGSGPAAHTAAIYAARAELKP
> LLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTK
> VDFSSKPFKLFTDS---KAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCD
> GAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKID
> VIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELD
> SDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEIGSQEGK
> SD-
> *
> >P1;fake1
> 
> DASGLSVAAAATLSQKSTPYYQSEIHTIGKRRMHSKVVIIGSGPAAHTAAIYLARAELKP
> VLYEGFMANGVAAGGQLTTTTEVENFPGFPEAVTGQELMDKMRAQSERFGTVIVSETVGK
> LDLSKRPFEYSTEWSPDTVMTADAVILATGASARRLGLPGED----KYWQNGISACAVCD
> GAVPIFRNKPLVVIGGGDSAAEEAIFLTKYGSHVTVLVRRDKLRASSIMARRLLAN----
> ------------------------------------------------------------
> -------------KKVTGLFAAGDVQDKRYRQAITSAGTGCMAALDAEKYLEELEDEQAD
> GKL
> *
> 
> Where should I stick the fad? At the end?  How many blk 
> characters should I tack on? 1 because there is only one 
> molecule? Is there a specific character for FAD?
> 
> These are my stumbling blocks.
> 
> regards
> 
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