Hi Geoff,
This is a great little widget . I just tried it and I think it is very
useful to directly communicate with RCSB via Jmol.
But, is there a way to directly homology model a protein sequence using the
RCSB to provide a best matching template such that the modeled structured
can be directly accessed in Jmol?
How difficult would this be to implement? May be Bob can tell us more.
Thank you! Merci beaucoup!
*AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami ,
FL 33136
[email protected] | off 305-243-2429 | lab 305-243-9799 | fax
305-243-3955 | www.farooqlab.net*
On Thu, Aug 22, 2013 at 12:52 PM, <[email protected]> wrote:
> Dear Jmol People,
>
> I've implemented a novel method for evaluating conserved protein
> features from databases such as CDD using JSmol. You can check it out
> here:
>
> http://bar.utoronto.ca/CDD3D
>
> The user submits a query protein sequence of interest to search for
> similar proteins from the RCSB or homology model databases. Selecting
> a related structure will populate JSmol (or Jmol if you choose) and if
> there are CDD features they will be mapped to the structure. To
> evaluate conservation, there are interactive alignments as HTML text
> that communicate directly with the structure model using Javascript.
>
> You can try for example this sequence:
>
> SVWRAINKQTGEVVAIKKMKKKYYSWDECINLREVKSLRRMNHPNIVKLKEVIRENDILYFVFEYMECNLYQLMKDRQKLFAEADIKNWCFQVFQGLSYMHQRGYFHRDLKPENLLVSKDIIKIADFGLAREVNSSPPFTEYVSTRWYRAPEVLLQSYVYTSKVDMWAMGAIMAELLSLRPIFPGASEADEIYKICSVIGTPTEETWLEGLNLANTINYQFPQLPGVPLSSLMPSASEDAINLIERLCSWDPSSRPTAAEVLQHPFFQSCFYVPPSLRPKPSVARTPPPVGPRGSFEHQSVKRYPVSLANAKPFNSYVSPKSNAAFGSGVQRKLDMVNQDGTRNTKPVRSSVRDSKYRPPGKKSPHNAAAASLNKNRVTRSSVSETADKLANMTIGATGSRRHSVSVVGQHQQLKPPPMKAGWVGETRDMFLRPTQ
>
> I'd be very happy to receive feedback!
>
> Perhaps you can help me with a problem - in JSmol the context menu is
> obscured for some reason that I can't figure out... probably something
> to do with the layout/CSS. Any help in this respect would be very much
> appreciated!
>
> Thank you all very much for your fantastic work on Jmol/JSmol.
>
> ~Geoff
>
> --
> Geoffrey Fucile, PhD
> Université de Genève
> Département de Biologie Moléculaire
> Sciences III
> 30 quai Ernest-Ansermet
> CH-1211 Genève 4
>
>
>
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