Now, I have a database of ~5k molecules with their names and SMILEs codes. I would like to convert the molecules from SMILEs format into 3D structure format (mol2) with right protonation states, multiple tautomeric states, atomic charges, atomic connectivity, valence, and if possible also chirality. I know DiscoveryStudio could handle these, but it is not free for academia.
1. Any packages could handle the molecule preparation well? Especially those with python API?
2. What else preparation protocols for a small molecule should be necessary for a docking task?
Thanks a lot!
obabel and babel are nice commandline tools for this ( https://openbabel.org/docs/dev/Command-line_tools/babel.html ).
A simple command to generate 3D coordinates and protonation states at pH 7.4 would be: obabel input.smi -O output.sdf --gen3d --p 7.4
There is also a python openbabel module ( http://openbabel.org/docs/current/UseTheLibrary/Python_Pybel.html).
Another python-based option is https://www.rdkit.org/docs/GettingStartedInPython.html.
Daniel Olp Thank you for the explanation, it is very helpful. I found that rdkit sometimes could not handle every molecule, for example, for 1000 SMILEs codes, rdkit could only generate ~800 molecules, 20% of the molecules could not be generated.
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