In this course, concepts of protein sequences and structure (construction and search), force fields, preparation of files to run a molecular dynamics, simulation using the NAMD program on your computer and analysis of the results are discussed. with VMD and the CARMA program.  

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TEMARY

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one.   Presentation.

two.   Protein structure.

3.   Application of molecular dynamics (DM) in the pharmaceutical area.

Four.   DM application in the biotechnology area.

5.   Generalities about Force fields.

6.   Concepts, (RMSD, RMSF, Rg, solvent accessible surfaces, conformational changes).

7.   Visualization exercises with VMD.

8.   Files required for a DM.

9.   Preparing files to run DM.

10.  Structure minimization for DM.

eleven.  DM simulation in NAMD.

12.  Continuation of DM simulation at NAMD.

13.  Analysis of results by VMD.

14.  Analysis of results by CARMA.

fifteen.  Continuation of analysis of results by CARMA.

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