Can anyone recommend a protocol for building the 3D structure of a small molecule de novo, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, then make conformers using Frog2. But I have no idea how realistic the starting structure is from PyMol and how exhaustively the conformers are sampled in Frog2.
The downstream application of this would be to dock the ligand into a protein binding pocket. If anyone has a more rigorous protocol for making sure all the conformational space is fully sampled, it would be greatly appreciated!