Biomolecular Simulation in Medicinal Chemistry and Toxicology

2018-2019
Dit vak wordt in het Engels aangeboden. Omschrijvingen kunnen daardoor mogelijk alleen in het Engels worden weergegeven.

Doel vak

Providing theoretical background on biomolecular simulation and
free-energy calculation methods and an overview of recent developments,
applications, and trends.

Inhoud vak

Methods 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
calculations.
Proper and efficient treatment of nonbonded intereactions: force field
development, boundary
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
their application.

Onderwijsvorm

Lectures, tutorials, exercises, and self-study.

Toetsvorm

Written or oral exam

Vereiste voorkennis

Course "Computational Design and Synthesis of Drugs"

Literatuur

Leach, A.R., Molecular Modelling: Principles and Applications. (ISBN
0-582-38210-6).
Recent review articles that will be made available via Canvas.

Doelgroep

mDDS

Overige informatie

Please contact the coordinator two weeks prior to the start of the
course (e-mail: d.p.geerke@vu.nl).

Aanbevolen voorkennis

Course "Computational Design and Synthesis of Drugs"

Algemene informatie

Vakcode X_432664
Studiepunten 6 EC
Periode P5+6
Vakniveau 400
Onderwijstaal Engels
Faculteit Faculteit der Bètawetenschappen
Vakcoördinator dr. D.P. Geerke
Examinator dr. D.P. Geerke
Docenten dr. D.P. Geerke
dr. C. de Graaf

Praktische informatie

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Werkvormen Hoorcollege
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