https://studiegids.vu.nl/en/courses/2024-2025/XM_0118Providing an overview of the theoretical background and application of molecular dynamics computer simulations in the context of drug discoveryMolecular Dynamics (MD) simulations are becoming increasingly important in in silico drug design. While static structures of protein-ligand complexes can be of great help in studying protein binding and interaction, a detailed understanding of drug action upon complexation may well require to explicitly account for the conformational flexibility of the protein and the dynamics of ligand binding. MD simulations can take on this role and be used to e.g. elucidate induced fit effects upon complexation, study kinetics of protein-ligand binding, and include entropic effects in affinity prediction. The theoretical part of this course consists of a series of lectures in which theory of and algorithms for MD simulation will be discussed, along with the models (force fields) to represent atomic interactions during simulation. In addition advanced sampling and (alchemical and end-point) methods will be presented that can be used to compute the free energy of e.g. protein-ligand binding from simulation. A major part of the course will focus on the use of MD and its application in a drug discovery context. In a first series of computer practicals students will be made familiar with setting up, running and analyzing MD simulations. Subsequently a small project will be performed in which MD will be used to study protein-ligand binding and interactions in the context of a pharmaceutically relevant application. Assessment of the written report on this application study will substantially contribute to the final grade of the course.Lectures, computer lab sessions (tutorials), working independent on a small projectWritten report on computer lab work, and a written or oral examLinks to relevant literature will be provided in advance and during thecoursemDDSBSc FAR course Molecular Modeling or MSc DDS course Principles of DrugDiscovery, or equivalent