Thanks to all for the replies,
I put an example for better explain my problem.
starting from a PDB representing HPE, I use RDKIT/obabel for calculate the
relative SMILES. Next, using a RDKIT's function I fragment the smiles in
substructure like this "CC(=O)O"; now I need to remap this substructure on
the starting tridimensional structureand in order to get the atom
coordinate. The task will be pretty easy if the numeration of the SMILES
atom representation is the same of the starting PDB file. You know any
methods to unify this two numeration? or to map the SMILES atom sequence on
the PDB's one?
This is the PDB for HPE.
HETATM 4176 N HPE B 2 5.227 20.107 15.512 1.00 17.92
N
HETATM 4177 CA HPE B 2 4.065 20.646 16.205 1.00 16.87
C
HETATM 4178 C HPE B 2 2.784 20.702 15.373 1.00 18.59
C
HETATM 4179 O HPE B 2 2.806 21.092 14.215 1.00 17.45
O
HETATM 4180 CB HPE B 2 4.377 22.085 16.699 1.00 17.52
C
HETATM 4181 CG HPE B 2 5.532 22.067 17.720 1.00 14.97
C
HETATM 4182 CD HPE B 2 5.886 23.416 18.279 1.00 17.87
C
HETATM 4183 CE1 HPE B 2 6.717 24.309 17.627 1.00 17.26
C
HETATM 4184 CE2 HPE B 2 5.385 23.752 19.520 1.00 19.20
C
HETATM 4185 CZ1 HPE B 2 7.025 25.546 18.162 1.00 17.16
C
HETATM 4186 CZ2 HPE B 2 5.698 24.993 20.061 1.00 22.45
C
HETATM 4187 CH HPE B 2 6.517 25.906 19.409 1.00 19.18
C
Thanks to all.
Carlo
On Wed, May 9, 2018 at 8:37 PM, Dimitri Maziuk <[email protected]>
wrote:
> On 05/09/2018 10:27 AM, carlo del moro wrote:
> > Dear All,
> >
> > we would like to know if it is possible to map the atom's ID of a SMILES
> > represented substructure to the atom sequence of a ligand contained in a
> > pdb file. This in order to get the spatial coordinates related to such
> > substructure.
>
> http://alatis.nmrfam.wisc.edu/ will generate unique stable IDs from a 3D
> structure, and output the old->new ID map. It'll take a PDB, you'll
> have to convert your SMILES into a 3D .mol. ALATIS atom IDs should be
> the same in the two maps, *provided both inputs describe the exact same
> ligand*.
>
> (It's the *substructure* bit that I'm not entirely sure about.)
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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