Molecule Preparation

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

Protonation

• DiMorphite-DL:
  
  
  
  

Reviews

• Sherman et al:
  

Standardization

• Ambitcli: no 3D but Java application for standardization (standalone).
  
• ChEMBL_Structure_Pipeline (formerly standardiser):
  
  
  
• 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).
  

Tautomer Generation

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

pKa

• Graph-pKa: Multi-instance learning of graph neural networks for aqueous pKa prediction (online)