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Energetics of protein structure

Energetics of protein structures. Molecular Mechanics force fieldsImplicit solventStatistical potentials. Energetics of protein structures. Molecular Mechanics force fieldsImplicit solventStatistical potentials. . What is an atom?. Classical mechanics: a solid objectDefined by its position (x,y,z), its shape (usually a ball) and its massMay carry an electric charge (positive or negative), usually partial (less than an electron).

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Energetics of protein structure

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    1. Energetics of protein structure

    2. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

    3. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

    4. What is an atom? Classical mechanics: a solid object Defined by its position (x,y,z), its shape (usually a ball) and its mass May carry an electric charge (positive or negative), usually partial (less than an electron)

    7. Atomic interactions

    8. Forces between atoms Strong bonded interactions

    9. Forces between atoms: vdW interactions

    11. Forces between atoms: Electrostatics interactions

    13. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

    14. Solvent Explicit or Implicit ?

    15. Potential of mean force

    16. Potential of mean force

    17. Potential of mean force

    19. The SA model Surface area potential

    20. Surface area potentials Which surface?

    21. Hydrophobic potential: Surface Area, or Volume?

    22. Elementary electrostatics Electrostatics in vacuo Uniform dielectric medium Systems with boundaries The Poisson Boltzmann equation Numerical solutions Electrostatic free energies The Generalized Born model

    23. Elementary Electrostatics in vacuo

    24. Elementary Electrostatics in vacuo

    25. Elementary Electrostatics in vacuo

    26. Elementary Electrostatics in vacuo

    27. Elementary Electrostatics in vacuo

    28. Elementary Electrostatics in vacuo

    43. Further reading Michael Gilson. Introduction to continuum electrostatics. http://gilsonlab.umbi.umd.edu M Schaefer, H van Vlijmen, M Karplus (1998) Adv. Prot. Chem., 51:1-57 (electrostatics free energy) B. Roux, T. Simonson (1999) Biophys. Chem., 1-278 (implicit solvent models) D. Bashford, D Case (2000) Ann. Rev. Phys. Chem., 51:129-152 (Generalized Born models) K. Sharp, B. Honig (1990) Ann. Rev. Biophys. Biophys. Chem., 19:301-352 (Electrostatics in molecule; PBE) N. Baker (2004) Methods in Enzymology 383:94-118 (PBE)

    44. Energetics of protein structures Molecular Mechanics force fields Implicit solvent Statistical potentials

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