OK, I am almost there!
First, I tried the AllChem.ConstrainedEmbed(qmol, core) function to
generate conformers, where core was a mol object created from the MCS with
3D coordinates copied from template's MCS. But is seems that this functions
works only when core is an intact molecule, because I ge
Hi Greg,
Many thanks for the awesome post! I am still having trouble though to
select the right reference ligand for each query molecule. In particular I
have 9 crystal ligands, so these are the possible scenarios given one query
compound:
1) Measure the overall fingerprint similarity between the
On Mon, Feb 20, 2017 at 6:17 PM, Thomas Evangelidis
wrote:
>
> Thank you for your useful hints. All the compounds that I want to align
> are supposed to belong to the same analogue series so they should shave a
> common substructure with substantial size.
>
In that case, using an MCS based align
Hello Thomas,
This publication could be of interest to you. I have not read the whole
paper so I don't know how relevant it is.
Ling
Graph-Based Molecular Alignment (GMA)
Marialke, Korner, Tietze, Apostolakis
J. Chem. Inf. Model. 47 (2007) 591-601
On Mon, Feb 20, 2017 at 3:32 PM, Thomas Evange
@Peter
I am working exactly on the scenario you described.
@Brian
I have found this thread which is pretty similar to my case and to what you
suggested, so now I am adapting my code accordingly.
https://sourceforge.net/p/rdkit/mailman/message/35034093/
What you have published sounds interesting.
With Glide, IIRC, this facility is designed for the use case where the
coordinates of a docked ligand are known (typically from an X-ray
structure) and the docked ligand shares a SMARTS with the ligands in an
input file. The SMARTS-matching atoms of each incoming ligand are
superposed upon the corr
I don't know the exact glide procedure, but I did write such a system for
OpenEye (POSIT). The issue you are facing is that the RMSD portion is just
a constraint used for docking, it isn't used as the "score", in fact, it
can't tell if the conformation interpenetrates the active site or which
orie
Greg and Brian,
Thank you for your useful hints. All the compounds that I want to align are
supposed to belong to the same analogue series so they should shave a
common substructure with substantial size.
What I want to emulate is the "core restrained docking" with glide, where
you specify the
I believe (Greg can correct me) to align the bemis-murcko scaffold, you
could
(1) extract the original atom pairs and send them to the RMSD algorithm
(2) take a bemis scaffold and convert it to a substructure query for use in
the RMSD algorithm. In either case the RMSD is the rmsd of the scaffold
HI Thomas,
To be sure we're talking about the same thing: rdMolAlign.GetO3A() is an
implementation of the Open3DAlign algorithm. This is an unsupervised
approach that uses a clever algorithm to come up with an atom-atom mapping
between the two molecules you give it. It's not always going to pick t
At least for the MCS calculation, there is an R package
for chemistry:
https://bioconductor.org/packages/release/bioc/vignettes/fmcsR/inst/doc/fmcsR.html
On 02/19/2017 07:33 PM, Thomas Evangelidis wrote:
> Dear all,
>
> I want to align 250 compounds that binding to the same pocket to one of
> the
As a follow up question on this topic, I would like to ask if
MurckoScaffold.GetScaffoldForMol(mol) returns the scaffold of mol with
different coordinates?
I am asking this because when I use the transformation matrix of the
alignment of the cores of the probe and the reference molecules, in order
12 matches
Mail list logo