MDExplorer tutorials adds a dedicated molecular dynamics pathway to the BASIL (biochemistry authentic scientific inquiry lab) curriculum, guiding students from structure prep through trajectory analysis so they can (1) generate conformational ensembles for improved docking and (2) extend promising protein-ligand complexes into MD simulations that reveal binding stability and mechanistic behavior. The open-source repository captures a 14-stage Python workflow that mirrors research-grade practice: structure preparation, topology generation, solvation, minimization, equilibration, long-timescale production, and protein-ligand analysis. Reusable utilities, VMD runners, and notebook companions guide learners from data ingestion through visualization while keeping outputs sandboxed in per-stage directories. Automated scripts (runₐll. py) and pytest suites ensure reproducibility across instructional and research modes, and utils/productionₘodes. py scales trajectories from 10 ns tutorials to 200 ns studies aligned with BASIL course timelines. Curriculum integration is supported by concise contributor guidance, HPC deployment notes, and web-facing extensions designed for an HTMX-powered interface. The project responds directly to goals documented in NSF IUSE Award 2142033, which funds the creation of a sustainable MD-enhanced docking module complete with representative ensembles, student assessments, and dissemination via workshops and educational publications. By combining executable notebooks, command-line automation, and modular analytics, MDExplorer tutorials equips faculty and students with a maintainable, platform-agnostic toolkit for exploring protein-ligand behavior and strengthens BASIL’s capacity to bridge classroom inquiry with modern computational biochemistry.
Kley et al. (Sun,) studied this question.