Using unpublished structures for template to create models?
Hi all,
I was hoping to get some help on the modeling of a protein target by sequence alignment using a 41% similar structure template I recently solved, in place of a published structure on the PDB. The resolution has changed and may help create a more accurate model for ligand docking. Thanks.
Geoff
Dr. Geoffrey Lippa Post-doctoral Research Associate Laboratory of Dr. Andrew Gulick Hauptman Woodward Medical Research Institute 700 Ellicott St., Buffalo, NY 14203 Phone: 585-690-0850 Email: glippa@hwi.buffalo.edu
Hi Geoff,
I wonder if Structuropedia might help: http://structuropedia.org
It is essentially MODELLER made simple. Give it a try. Just copy and paste your sequence. Simple as that.
With warmest regards,
*AMJAD FAROOQ PhD DIC | Associate Professor*Dept of Biochemistry, University of Miami School of Medicine *Location*: Gautier Building, Suite 217 *Address*: 1011 NW 15th Street #217, Miami , FL 33136, USA *Contact*: amjad@farooqlab.net | 305-243-2429 *Labpage*: farooqlab.net | structuropedia.org
On Wed, Dec 10, 2014 at 5:22 PM, Geoffrey Lippa glippa@hwi.buffalo.edu wrote:
> Hi all, > > I was hoping to get some help on the modeling of a protein target by > sequence alignment using a 41% similar structure template I recently > solved, in place of a published structure on the PDB. The resolution has > changed and may help create a more accurate model for ligand docking. > Thanks. > > Geoff > > > Dr. Geoffrey Lippa > Post-doctoral Research Associate > Laboratory of Dr. Andrew Gulick > Hauptman Woodward Medical Research Institute > 700 Ellicott St., Buffalo, NY 14203 > Phone: 585-690-0850 > Email: glippa@hwi.buffalo.edu > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
On 12/10/14 2:22 PM, Geoffrey Lippa wrote: > I was hoping to get some help on the modeling of a protein target by > sequence alignment using a 41% similar structure template I recently > solved, in place of a published structure on the PDB. The resolution > has changed and may help create a more accurate model for ligand > docking.
You don't have to do anything special to use an unpublished structure as a template. Just save it in PDB format and then proceed normally.
Ben Webb, Modeller Caretaker
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Modeller Caretaker