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RxDock is a fast and versatile open-source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and binding mode prediction studies.

JAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.