Re: [Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

[Paolo Tosco]

Dear Steven,

just to add up a small bit to Maciek's reply, you may find some examples 
how to use the RDKit MMFF94 C++ API in 
Code/ForceField/MMFF/testMMFFForceField.cpp and in 
Code/ForceField/MMFF/testMMFFHelpers.cpp.
All of the constraints are available from C++, a search for "fixed 
atoms" in Code/ForceField/MMFF/testMMFFForceField.cpp will point you to 
an example how to set fixed atoms.


To minimize a ligand in the context of a protein pocket I would combine 
the ligand and the relevant residues in a ROMol, set the desired 
contraints and then minimize. Please do not hesitate to get back to me 
if you run into trouble.


Cheers,
p.


On 01/04/2016 16:29, Steven Combs wrote:

Hi,

Is it possible to do a minimization in mmFF in context of two 
small-molecules or a single small molecule and sidechains from a 
binding pocket? From what I gather, I have two options:


1) Make a single RWMol object with the ligand and all residues from 
the binding pocket, then run mmFF on the combine molecule. The steps 
would look like this

   -use combineMols() for all residues
   -use mmFF on the complex

2) Use a hacked version of MCS from here: 
http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html



Is there a better way of doing this? I am using the C++ api.

Steven Combs


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Re: [Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

[Maciek Wójcikowski]

Hi Steven,

No. 1) is exactly what I'm doing to preform rigid protein minimization of
ligands. I use ff.AddFixedPoint() to fix all protein atoms (you could omit
the desired side chains). For better performance I also use following
params:

ff = AllChem.MMFFGetMoleculeForceField(comp, ff_mp, nonBondedThresh=10.,
ignoreInterfragInteractions=False)

where comp is complex Mol, ff_mp are force-field molecular properties.

PS. There is no C++ API to my knowledge, although Greg/Paolo might have
something in his undocumented wizard hat ;)


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-04-01 17:29 GMT+02:00 Steven Combs :

> Hi,
>
> Is it possible to do a minimization in mmFF in context of two
> small-molecules or a single small molecule and sidechains from a binding
> pocket? From what I gather, I have two options:
>
> 1) Make a single RWMol object with the ligand and all residues from the
> binding pocket, then run mmFF on the combine molecule. The steps would look
> like this
>-use combineMols() for all residues
>-use mmFF on the complex
>
> 2) Use a hacked version of MCS from here:
> http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html
>
>
> Is there a better way of doing this? I am using the C++ api.
>
> Steven Combs
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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[Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

[Steven Combs]

Hi,

Is it possible to do a minimization in mmFF in context of two
small-molecules or a single small molecule and sidechains from a binding
pocket? From what I gather, I have two options:

1) Make a single RWMol object with the ligand and all residues from the
binding pocket, then run mmFF on the combine molecule. The steps would look
like this
   -use combineMols() for all residues
   -use mmFF on the complex

2) Use a hacked version of MCS from here:
http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html


Is there a better way of doing this? I am using the C++ api.

Steven Combs
--
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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140___
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