Question: Pdb File Of Drug
1
gravatar for Surendrs
3.2 years ago by
Surendrs10
Surendrs10 wrote:

hello friends

can anyone help to tell how to get pdb file of drug molecule?

surendra

ADD COMMENTlink modified 3.2 years ago by Nir London210 • written 3.2 years ago by Surendrs10
3
gravatar for Egon Willighagen
3.2 years ago by
Maastricht
Egon Willighagen4.6k wrote:

You can download 3D models for drugs from many databases, including PubChem, ChemSpider, and DrugBank. You can then use OpenBabel to convert those models into PDB files.

ADD COMMENTlink written 3.2 years ago by Egon Willighagen4.6k
2
gravatar for Michael Kuhn
3.2 years ago by
Michael Kuhn4.7k
Dresden, Germany
Michael Kuhn4.7k wrote:

What do you mean? Drugs as they have been found to bind to proteins? In this case, the SuperLigand database might help you (e.g. ibuprofen). There's also the subscription-based Cambridge Structural Database. Lastly, a Google search finds DrugPort (e.g. ibuprofen).

ADD COMMENTlink written 3.2 years ago by Michael Kuhn4.7k
1
gravatar for Nir London
2.9 years ago by
Nir London210
Nir London210 wrote:

If I understand correctly, surendra, you managed to convert to PDB but failed to view it in Discovery Studio? Perhaps try to convert it to a mol2 file (if it's not already the native format) and that would go through better.

ADD COMMENTlink written 2.9 years ago by Nir London210
0
gravatar for Surendra
3.2 years ago by
Surendra0
Surendra0 wrote:

thanks Egon W and M Kuhn for giving answer,, @ Egon as you told me download 3d model and then convert into pdb files,,,it does work,,i got coordinates of my drug in openbabel software ,,, but i got stuck when these pdb files converting into pdb viewer.my question is how do we convert these pdb files coordinates into pdb viewer? i have discovery studio software for viewing pdb files.i am not able to convert these file coordinates into pdb form for further use.

ADD COMMENTlink written 3.2 years ago by Surendra0

Please explain what you mean with converting a PDB file into a PDB viewer... and I do not get if you managed to create a PDB file or not...

ADD REPLYlink written 3.2 years ago by Egon Willighagen4.6k
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