Oregon State University 3 credits BB
Introduces computational modeling of biomolecules, including proteins and lipids. Examines basic principles of physics-based approaches such as molecular dynamics (MD), docking, atomistic vs. coarse-grained descriptions of molecules, and balance between chemical accuracy and adequate exploration of length/time-scales. Investigates force-field parametrization from thermodynamic data, experiments, and quantum mechanical data. Considers tools for creating simulation inputs and processing of structural files (e.g., protein databank), basic usage of open-source MD simulation packages, data processing, analysis of simulation trajectories, and visualization of molecular models. Examines practical usage of AlphaFold/RosettaFold for developing starting structures for MD simulations.
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