ALL LECTURES

  1. Introduction
  2. Molecular Architecture I
  3. Molecular Architecture II
  4. Bioinformatics I
  5. Bioinformatics II
  6. Molecular Simulation I
  7. Molecular Simulation II

CONCEPTS IN THIS LECTURE

Molecular Simulation II

  1. Normal Mode theory
  2. Protein Normal Modes
  3. Unfolding alpha Helix
  4. Unfolding Proteins
  5. Folding Simplified Chains
  6. Folding Simulations

5. Molecular Simulation II

5.1. Normal Mode theory

5.2. Protein Normal Modes

  1. SB228 Lecture 5 Lecture5
  2. Molecular Simulation II
  3. Normal Mode theory. Concept 5.1
  4. Normal Mode Dynamics
  5. Basic theory
  6. Normal Modes in High Dimensions1
  7. Normal Modes in High Dimensions2
  8. Normal Modes in High Dimensions3
  9. Molecular Potential Energy
  10. Potential Energy in torsion Space
  11. Theory of Normal Modes I
  12. Theory of Normal Modes II
  1. Protein Normal Modes. Concept 5.2
  2. Rates of Vibration
  3. Amplitudes of Vibration
  4. Trypsin inhibitor Modes
  5. BPTI Normal Modes Movie
  6. Lysozyme Modes
  7. Lysozyme Normal Modes Movie
  8. Ribonuclease Modes
  9. Ribonuclease Normal Modes Movie

5.3. Unfolding alpha Helix

5.4. Unfolding Proteins

  1. Unfolding alpha Helix. Concept 5.3
  2. Alpha-Helix Unfolding
  3. Why Simulate Unfolding
  4. Unfold alpha-Helix
  5. Effect of Temperature
  6. Helix Less Stable in Water
  7. Water allows Hydrogen Bonds to Break
  8. Helix Unfolding Movie
  9. Distributions in Solution
  1. Unfolding Proteins. Concept 5.4
  2. Protein Unfolding
  3. What Happens to Secondary Structure
  4. Protein Unfolding1 Movie
  5. What Happens to aromatic Sidechains
  6. Protein Unfolding2 Movie
  7. Unfolding Pathway
  8. Connection to Experiment1
  9. Connection to Experiment2
  10. Connection to Experiment3

5.5. Folding Simplified Chains

5.6. Folding Simulations

  1. Folding Simplified Chains. Concept 5.5
  2. Fold Simplified Proteins
  3. Why is Folding So Difficult
  4. Simplified Models for Folding1
  5. Virtual Bonds
  6. Simplified Models for Folding2
  7. Cartoon Folding Movie
  8. 3x3x3 Cube Protein Folding
  9. Lattice Model of Folding
  1. Folding Simulations. Concept 5.6
  2. Folding Simulations
  3. Need Massive Computational Resources
  4. Villin Folding
  5. IBM Blue Gene Project
  6. IBM Blue Gene Design
  7. Folding at Home
  8. Folding at Home Helix Folding
  9. Pande Helix Folding Movie
  10. Pande Villin Folding Movie
  11. Folding at Home Rates