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BLU 604E
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Course Information
Course Name
Turkish
Moleküler Dinamik Simülasyonlarıİçinİleri AnalizYöntemleri
English
Adv.Ana.Tec.for Mol.Dyn.Simu.
Course Code
BLU 604E
Credit
Lecture
(hour/week)
Recitation
(hour/week)
Laboratory
(hour/week)
Semester
-
3
3
-
-
Course Language
English
Course Coordinator
Sefer Baday
Course Objectives
1)Teaching applications of MD simulation in biomembrane applications
2)Teaching advanced methods for analyzing MD simulation trajectories
3)Teaching usage of programs and codes developed for analyzingMD simulation results
Course Description
Applications of MDSimulationsin biomembrane dynamics and function studies.Performing MD Simulations with NAMD program.VMD: a MD simulation analysis program.Time series analysis of basic features: Hydrogen bond, secondary structure, angle and distance.Root Mean Square Deviation (RMSD) andRoot Mean Square Fluctuation (RMSF) calculations.Radial distribution function (RDF) and radius of gyration calculations.Principal component analysis of MD trajectory.Cross-correlation analysis.Elastic Network analysis of MD trajectories.Methods for analyzing simulations of Biomembranes and Membrane proteins.Density and diffusion calculations.Interaction Energy calculations of MD trajectories.MD simulation analysis using Markov State models-1.MD simulation analysis using Markov State models-2
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