I. Course Description
Understanding protein dynamics and computational techniques developed to study the
motions/conformational changes of biomolecules; basic math, physics and computer
simulation techniques are conferred in the regular course as well as dedicated
workshops (need based)

II. Text Books
Molecular Modeling - Principles and Applications, by Andrew R Leach

III. References
"Biochemistry, 5th edition", by Garrett & Grisham. Publisher: Thomson/Brooks/Cole
“Molecular Biophysics”, by Daune
“Structural Bioinformatics” by Jenny Gu, Philip E. Bourne
“Normal Mode Analysis”by Qiang Cui & Ivet Bahar
“Coarse-Graining of Condensed Phase and Biomolecular Systems”by Gregory A Voth
Math Chapters (Appendix) in "Quantum Chemistry" by Donald McQuarrie

IV. Teaching Method
Lectures plus after-class hands-on practice in programming and using computer
software (including but not limited to Linux, VMD, AMBER, NAMD, Matlab)

V. Syllabus
Motions, dynamics, protein dynamics, dynamics and functions, protein databank
(PDB),
a few words about structure biology
MD simulations I (Newtonian mechanics)
MD simulations II
Elastic Network Model - ANM
Normal Mode Analysis
Elastic Network Model - GNM
Monte Carlo simulations
Coarse-Grained MD simulations
Targeted and Steered MD Simulations
Free Energy Calculations
Replica Exchange MD Simulations
Non-equilibrium dynamics (e.g. Linear Response Theory, MD, MC, replica exchange)
Electrostatics – Ewalds Methods
Implicit solvent - solvation energy calculations using Generalized Born/Poisson
Boltzmann
Entropy Calculation

VI. Evaluation
Student delivering one or two Lectures on subjects related to protein dynamics
(80%)
Homework (20%) (on simulation and protein modeling)