ADL: PDB preparation best practices for Vina?

Mark Pohl mark.pohl at licensinglaw.net
Tue Dec 22 09:54:09 PST 2020


The content is there.  The email below has a typographical error in it.  The link is http://vina.scripps.edu/tutorial.html, not http://vina.scripps.edu/tutorial.htmlThe.  
If you've further problems, let me know!
Mark Pohl, Esq.
Pharmaceutical Patent Attorneys, LLC   
55 Madison Avenue, 4th floorMorristown, NJ 07960-7397  USA
+1 (973) 984-6159 x304
 

    On Tuesday, December 22, 2020, 11:27:02 AM EST, Drasko Tomic <drasko.tomic at yahoo.com> wrote:  
 
 Dear Mark,
seems there is no content there:

The requested URL /tutorial.htmlThe was not found on this server.
ADDRESS:
Apache Server at vina.scripps.edu Port 80

Regards,

Drasko



    On Thursday, December 17, 2020, 9:00:18 PM GMT+1, Mark Pohl <mark.pohl at licensinglaw.net> wrote:  
 
 Oleg Trott, the graduate student who wrote VINA, made a nice (albeit somewhat dated) video:  http://vina.scripps.edu/tutorial.htmlThe same page provides a link to his test files, so you can follow along with his lecture. 
Hope this helps!
Mark Pohl, Esq.
Pharmaceutical Patent Attorneys, LLC   
 

    On Wednesday, December 16, 2020, 8:12:39 PM EST, Francois Berenger <mlists at ligand.eu> wrote:  
 
 Hello,

I think chimera has a nice docking tutorial:

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html

http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm

Maybe there is the same thing for Vina somewhere.

Regards,
F.

On 15/12/2020 20:13, Rick Sheridan wrote:
> Hello -
> 
> Does anyone know of a preferred go-to reference checklist for preparing 
> a
> protein from the PDB for docking in Vina?  For example it might include
> steps like 'remove any ligands the model is already in complex with' or
> 'determine if any solvent molecules are part of the protein's 
> structure' or
> managing polar vs non-polar hydrogens.
> 
> Best,
> Rick
> 
> --


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