JAMDAscorer

Overview

JAMDAscorer post-optimizes protein-ligand complexes into precise local energy minima with the new JAMDA scoring function. This new empirical scoring function can be used with gradient-based optimizers. By combining it with the optimizer LSL-BFGS, fast convergence, locality, and the precise detection of local minima are guaranteed. JAMDAscorer considers hydrogen bond geometries, hydrophobic contacts, clashes, and torsion angles. Therefore, it balances the most relevant terms in protein-ligand scoring functions.

Software Availability

The command-line tool JAMDAscorer is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download JAMDAscorer, 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 JAMDAscorer. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

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