Molecule Preparation

Gypsum-DL: Gypsum-DL is a software that transforms 1D and 2D small-molecule representations into 3D models, considering various isomeric and conformational states.
Spores: check structure, protonation (standalone).

Protonation

DiMorphite-DL: Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

Sherman et al: Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

Ambitcli: no 3D but Java application for standardization (standalone).
ChEMBL_Structure_Pipeline (formerly standardiser): An open source chemical structure curation pipeline using RDKit
MolVS:
QSAR-Ready (KNIME): Standardization workflow for QSAR-ready chemical structures pretreatment
Standardiser: standardize molecules, it requires RDKIt (standalone).
Standardize: PubChem chemical structure standardization (online).
Standardized-smiles: Python script to standardize small molecules (use RDKIT) (standalone).

MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution (compound preparation) (standalone).

Graph-pKa: Multi-instance learning of graph neural networks for aqueous pKa prediction