ADL: command-line or programmatic method for detailing ligand:protein contacts?

Oleg Trott trott at scripps.edu
Tue Nov 12 15:59:52 PST 2013


Hi

That's correct for the best (i.e. first) binding mode. It's more
complicated for other binding modes, where you have to think about the
"reference state" for the internal "energy". The Vina paper tries to
explain this.

On Thu, Nov 7, 2013 at 10:22 PM, Dennis N Bromley <dbromley at uw.edu> wrote:
> thank you, everyone, I really appreciate the help.
>
> Oleg, will the number returned when using your --score-only suggestion be a
> subset of the overall docking score i.e. if the overall docking score is -7
> kcal/mol and the --score-only value with most of the residues stripped away
> is -5 kcal/mol, does that imply that 5/7 of the binding energy came from
> those remaining residues?  It's a cool idea, I am just trying to understand
> the enthalpic and entropic contributions under those kind of funny
> conditions.
>
> thanks again, everybody.  One step closer to graduation...
> -denny-
>
>
>
>
>
> On Thu, Nov 7, 2013 at 4:24 PM, Matt Ketterer <mketterbob at gmail.com> wrote:
>
>> I wrote some code awhile back using Openbabel, which picked out close
>> contacts, using Python, then wrote them out into a file, such as a csv.
>>  Let me know if you want it and I can email it to you.  You would have to
>> be able to know a bit of python, or I can help you with a little bit of
>> manipulation it shouldn't take too long.
>>
>> Matt
>>
>>
>> On Thu, Nov 7, 2013 at 6:28 PM, Oleg Trott <trott at scripps.edu> wrote:
>>
>> > Hi
>> >
>> > I think AutoDock Raccoon 2 does that. Alternatively, you could
>> > manually remove everything from the receptor except the residues in
>> > question, run
>> >   "vina --score_only ..."
>> > on the docking results, which is essentially instant, and select the
>> > results that still give you good "energy".
>> >
>> > On Thu, Nov 7, 2013 at 10:13 AM, Dennis N Bromley <dbromley at uw.edu>
>> wrote:
>> > > Hi all,
>> > >
>> > > Thank you for your help recently.  I now have a pile of thousands of
>> > docked
>> > > ligands and proteins and I need to analyze them for specific contacts
>> > e.g.
>> > > how many of these 10,000 vina files show ligand hydrogen bonds to L123
>> > and
>> > > electrostatic contacts with G201?
>> > >
>> > > Can anyone recommend a good tool for doing this?  I don't mind parsing
>> up
>> > > thousands of log files if there is a tool that will create those.  I
>> just
>> > > can't sit there for months using a GUI and doing it all by eye.
>> > >
>> > > thanks!
>> > > -denny-
>> > > ________________________________________________
>> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
>> >
>> >
>> >
>> > --
>> > Oleg Trott, Ph.D. (Columbia University)
>> >
>> > Staff Scientist in the Olson Lab
>> > The Scripps Research Institute
>> >
>> > http://olegtrott.com
>> > ________________________________________________
>> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>> >
>> ________________________________________________
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>>
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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