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I converted a .pdb file to a .MOL file through BABEL (Converter Software). I do get the .MOL file, but when I submit the file online for a similar structure search It doesn't even load the file in ChemSpider.

To use PubChem's database you need SMILES format, which BABEL cannot properly convert my .pdb file to. So I'm out of luck there.

Any way I can search my .MOL file on any chemical database that's out there?

Thanks

SweetJD14
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    did you convert the ligand or the whole protein? – Maximilian Peters May 03 '16 at 08:12
  • You can certainly convert .mol files to SMILES using babel, also you can just use mol files directly in pubchem, so... – gilleain May 04 '16 at 07:52
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    As a meta-comment, I should point out that you might get more/better answers to questions like this on the biology/chemistry stack exchanges, or on biostars.org. Unfortunately, technology questions specific to science fall between the cracks a bit, so I understand that it's difficult :/ – gilleain May 04 '16 at 08:23

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