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computational molecular biophysics

J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague

Meterials for students

Materials for the course "Basics of Molecular Simulations" taught at the Charles University, Prague.

Course codes: NBCM051 (MFF UK) & MC260P79 (PřF UK)

Lecturs (winter semester 2017/2018): each Wednesday, 10:40am, Ke Karlovu 3, Praha 2, Seminarni mistnost KCHFO (suteren).
First lecture: October 4th, 2017

MD Lab exercises: November 29 & December 13, 2017, Ke Karlovu 3, room M-145 (36) (suteren). For MD lab materials, see below.

Consultations: January 10, 2018, 10:00-11:00, Institute of Organic Chemistry and Biochemistry CAS, Flemingovo nam. 542/6, Prague 6 Dejvice, room A.3.14.

This course is best suited for master and doctoral students at MFF and PřF UK

It is practically-oriented, topics range from physical chemistry to biophysics with the focus on the latter.

The topics include:

  • Physical basis of molecular interactions
  • Methods and algorithms used in modern molecular MD simulations
  • Practical examples of simulations for various biophysical systems
  • Data analysis and visualization, including modern Big Data and machine learning techniques

Applications of MD simulations to biological, pharmaceutical, and medical problems will be discussed.

For example:

  • Localization and action of small drug molecules in cellular membranes
  • Drug permeability across membranes
  • Drug-protein interactions
  • Molecular drug delivery systems
  • Ageing - lipids under oxidative stress, apoptosis
  • Implants biocompatibility

Lecture notes (individual links will become available during the semester):

  • Lecture 1, Introduction: link
  • Lecture 2, Force fields: link
  • Lecture 3, Integrators: link
  • Lecture 4, PBC, cutoffs, PME: link
  • Lecture 5, Neighbours, constraints: link
  • Lecture 6, Ensembles: link
  • Lecture 7, Simulation protocol: link
  • Lecture 8, Analysis: link
  • Lecture 9, Monte Carlo & Docking: link
  • MD Lab materials: link
    Note! Attending and passing the MD Labs is obligatory in order to pass the course. The MD Labs take place Nov 29 & Dec 13 2017 (from 10:40am till 1:40pm ) at Počítačová laboratoř Karlov (link)

Papers for dicussion (individual links will become available during the semester):

Python examples (Jupyter Notebooks):