JAMDA

Overview

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.

Software Availability

Up to five small molecule ligands can be prepared and docked into ligand-bound or predicted binding sites on our ProteinsPlus web service. Please visit https://proteins.plus, upload your protein, and choose JAMDA.
The command-line tool JAMDA is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download JAMDA, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run JAMDA. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Flachsenberg, F.; Ehrt, C.; Gutermuth, T.; Rarey, M. Redocking the PDB. J Chem Inf Model 2024, 64 (1), 219-237. DOI: https://doi.org/10.1021/acs.jcim.3c01573
Flachsenberg, F.; Rarey, M. LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. J Comput Chem 2021, 42 (15), 1095-1100. DOI: https://doi.org/10.1002/jcc.26522
Flachsenberg, F.; Meyder, A.; Sommer, K.; Penner, P.; Rarey, M. A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. J Chem Inf Model 2020, 60 (12), 6502-6522. DOI: https://doi.org/10.1021/acs.jcim.0c01095