OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein-Ligand Systems in OpenMM.
Journal of chemical information and modeling February 24, 2025 Valerij Talagayev, Yu Chen, Niklas Piet Doering et al. 16 citations
OpenMMDL is a new open-source toolkit that extends the molecular dynamics software OpenMM with modules for building, simulating, and analyzing protein-ligand complexes. It comprises three components: a graphical setup interface, a simulation module with trajectory postprocessing, and an analysis module that tracks ligand binding modes and clusters water molecules with minimal displacement. The toolkit was applied to seven diverse biological systems: kinases (ALK2 with LDN-193189 and LDN-212854), ion channels (Cav1.1 with nifedipine and amlodipine), G-protein coupled receptors (5-HT2B with LSD), cytochrome P450 oxygenases (CYP19A1 with letrozole), an RNA riboswitch (FMN-riboswitch with flavin mononucleotide), toll-like receptor 8 (TLR8 with ligand C08), and the opioid receptor (MOR with PZM21). OpenMMDL is publicly available on GitHub.