History___Basics_Handout

# History___Basics_Handout - Molecular Modeling History and...

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1 Molecular Modeling: History and Basic Concepts BIOL 7110 / CHEM 8901 / BIOL 4105 / 4804 February 10, 2011 Molecular Mechanics Models Molecular modeling on a computer: Not just molecular graphics Use models pedagogically: Explain what is known Use models predictively: Develop experimentally testable hypotheses Specify x,y,z coordinates of each atom Calculate energy as a function of conformation We “build” models We “refine” or “optimize” models We “run simulations”

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2 Molecular Mechanics Models: Two Major Classes Modeling is essential for solving some experimental problems Models can be used to solve problems that can’t be solved experimentally Structure refinement: x-ray crystallography NMR cryo-electron microscopy De novo model building Modeling is used as a supplement to experimental approaches Interpretation of structural data: x-ray crystallography NMR cryo-electron microscopy simulations THEME 1: Similarities and differences between structure refinement and de novo modeling. Structure refinement: Modeling is driven by experimental data (often supplemented by a molecular mechanics energy function). Goal: Determine the structure. modeling (ab initio modeling): Modeling is driven by a molecular mechanics energy function (sometimes supplemented by experimental data). Predict the properties of the molecule. Holy grail: Predict macromolecular structures.
3 Molecular Structure and X-ray Diffraction When x-rays are scattered from an object with an ordered, repeated structure, the resulting diffraction pattern is also ordered. What arrangement of the atoms in 3D space is consistent with the diffraction pattern? Some materials are fibrous (silk). Some molecules can be drawn into fibers (DNA). Fiber diffraction patterns from such materials give low resolution structures . Some molecules can be crystallized. Crystal diffraction patterns contain sufficient information to provide structures at atomic resolution . Need Models!

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## This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Tech.

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History___Basics_Handout - Molecular Modeling History and...

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