Course ObjectiveProviding theoretical background on biomolecular simulation and
free-energy calculation methods and an overview of recent developments,
applications, and trends.
Course ContentMethods and techniques for calculating molecular energies of
biomolecular systems (molecular mechanics / force fields) and for
flexibility analysis (conformational search methods).
Theory (statistical mechanics), method development (algorithms) and
application of molecular dynamics simulations and free energy
Proper and efficient treatment of nonbonded intereactions: force field
conditions, long-range forces.
Analysis of simulation data: secondary structure, solvation and
thermodynamic properties, transport and correlation.
Special focus on methods to predict binding affinities from MD
simulation (thermodynamic integration, free energy perturbation) and
Teaching MethodsLectures, tutorials, exercises, and self-study.
Method of AssessmentWritten or oral exam
Entry RequirementsCourse "Computational Design and Synthesis of Drugs"
LiteratureLeach, A.R., Molecular Modelling: Principles and Applications. (ISBN
Recent review articles that will be made available via Canvas.
Additional InformationPlease contact the coordinator two weeks prior to the start of the
course (e-mail: firstname.lastname@example.org).
Recommended background knowledgeCourse "Computational Design and Synthesis of Drugs"
|Language of Tuition||English|
|Faculty||Faculty of Science|
|Course Coordinator||dr. D.P. Geerke|
|Examiner||dr. D.P. Geerke|
dr. D.P. Geerke
dr. C. de Graaf
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