Open Babel
The chemistry toolbox for converting molecular formats
Open Babel is the universal translator of chemistry file formats, supporting over 100 formats plus substructure search, fingerprints and 3D coordinate generation.
Example
1obabel ligand.smi -O ligand.pdbqt --gen3d
Often used to prepare ligands for docking with AutoDock Vina.
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RDKit
The open-source cheminformatics toolkit
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AutoDock Vina
Fast, widely used molecular docking
Command linePython library