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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.
    Code Last Commit

    Publication JIF

  • Spores: check structure, protonation (standalone).

Protonation

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

    Publication JIF

Reviews

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

    Publication JIF

Standardization

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

  • ChEMBL_Structure_Pipeline (formerly standardiser): An open source chemical structure curation pipeline using RDKit
    Code Last Commit

    Publication JIF

  • MolVS:
    Code Last Commit

  • QSAR-Ready (KNIME): Standardization workflow for QSAR-ready chemical structures pretreatment
    Code Last Commit

  • Standardiser: standardize molecules, it requires RDKIt (standalone).
    Code Last Commit

  • Standardize: PubChem chemical structure standardization (online).

    Webserver

  • Standardized-smiles: Python script to standardize small molecules (use RDKIT) (standalone).
    Code Last Commit

Tautomer Generation

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

    Webserver

pKa

  • BCL_XpKa: Interpretable Deep-Learning pKa Prediction for Small Molecule Drugs
    Code Last Commit

    Publication JIF

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

    Publication JIF