rdock-list-def Mailing List for rDock

Dear Oscar,

rDock only takes into account full flexibility for the ligand.
However, terminal OH and NH3+ groups within RECEPTOR_FLEX distance of the
cavity defined will also be considered as flexible.
In section 8.1 of the documentation you have some more details about this
parameter:

RECEPTOR FLEX: Defines terminal OH and NH3+ groups within this distance of
docking volume as flexible. (default: 0, reasonable value: 3)

Best,

Sergio Ruiz


2015-05-19 12:03 GMT+02:00 Oscar Huertas <hu...@so...>:

> Hi all!
>
> I would like to know if is possible to run docking leaving some residues
> of the protein flexible or if is only possible with rigid protein.
>
> Thank you in advance for your answer.
>
> Oscar
>
>
>
>
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Hi all!

I would like to know if is possible to run docking leaving some residues of
the protein flexible or if is only possible with rigid protein.

Thank you in advance for your answer.

Oscar 

 



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Hi Jose,

Exactly!  Personally, I use the SCORE term when I rank poses.  Now for
ranking compounds against each other, sometimes I use the SCORE term other
times I use the SCORE.INTER.  I typically pick whatever seems to correlate
with my data the most strongly (either my own, or things I find in
published articles).

Hope that helps!
Matthew


On Tue, May 12, 2015 at 7:53 AM, Jose Manuel Gally <
jos...@un...> wrote:

> Hi,
>
> I am scratching my head about when I should use rather SCORE or
> SCORE.INTER to get the best poses per ligand...
>
> In the ROC curve tutorial (1), the SCORE is used to sort the poses and
> get the best pose per ligand whereas SCORE.INTER is used to plot the ROC
> curve.
> In the HTVS tutorial (2), only SCORE.INTER is used to determine the best
> ligands at each step.
> In this thread (3) , Sergio explains how to get the top unique ligands
> with both scores.
>
> Is SCORE.INTER enough to determine the best poses per ligand? In what
> case is it better to use SCORE rather than SCORE.INTER?
>
>  From what I understood by reading the reference guide, SCORE.INTER is
> the weigthed sum of intermolecular interections and so represents the
> protein-ligand interactions, whereas SCORE represents the sum of all
> other scores (total score)...
>
> Thank you for your answer!
>
> Jose Manuel
>
> REFERENCES:
> (1) http://rdock.sourceforge.net/how-to-calculate-roc-curves/
> (2) http://rdock.sourceforge.net/multistep-protocol-for-htvs/
> (3) http://sourceforge.net/p/rdock/mailman/message/32567916/
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

Hi,

I am scratching my head about when I should use rather SCORE or 
SCORE.INTER to get the best poses per ligand...

In the ROC curve tutorial (1), the SCORE is used to sort the poses and 
get the best pose per ligand whereas SCORE.INTER is used to plot the ROC 
curve.
In the HTVS tutorial (2), only SCORE.INTER is used to determine the best 
ligands at each step.
In this thread (3) , Sergio explains how to get the top unique ligands 
with both scores.

Is SCORE.INTER enough to determine the best poses per ligand? In what 
case is it better to use SCORE rather than SCORE.INTER?

 From what I understood by reading the reference guide, SCORE.INTER is 
the weigthed sum of intermolecular interections and so represents the 
protein-ligand interactions, whereas SCORE represents the sum of all 
other scores (total score)...

Thank you for your answer!

Jose Manuel

REFERENCES:
(1) http://rdock.sourceforge.net/how-to-calculate-roc-curves/
(2) http://rdock.sourceforge.net/multistep-protocol-for-htvs/
(3) http://sourceforge.net/p/rdock/mailman/message/32567916/