ADL: PDB preparation best practices for Vina?

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ADL: PDB preparation best practices for Vina?

Rick Sheridan
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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Rick Sheridan
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Re: ADL: PDB preparation best practices for Vina?

Francois Berenger
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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Re: ADL: PDB preparation best practices for Vina?

Mark Pohl
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 <[hidden email]> 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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Re: ADL: PDB preparation best practices for Vina?

Drasko Tomic
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 <[hidden email]> 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 <[hidden email]> 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
>
> --


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
 
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---  
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Re: ADL: PDB preparation best practices for Vina?

Mark Pohl
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>
> --


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
 
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---    
________________________________________________
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