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
  8. Prediction I
  9. Prediction II

CONCEPTS IN THIS LECTURE

Prediction II

  1. Fold Recognition
  2. Fold Recognition at CASP
  3. Progress at CASP
  4. Early ab initio Prediction
  5. Modern New Fold Prediction
  6. Winning NF Methods at CASP

9. Prediction II

9.1. Fold Recognition

9.2. Fold Recognition at CASP

  1. SB228 Lecture 9 Lecture9
  2. Structure Prediction II
  3. Fold Recognition. Concept 9.1
  4. Fold Recognition
  5. Comparative Modeling vs Threading
  6. Threading Covers More of Protein Space
  7. What is Fold Recognition
  8. What is Threading
  9. Simple Example
  10. A Different Threading
  11. Gaps in Threading
  12. Frozen approximation
  13. Use a Sequence Profile
  14. Profile Matching1
  15. Profile Matching2
  16. Deletions Using Structure
  17. Insertions Using Structure
  18. Getting Good alignments Summary
  1. Fold Recognition at CASP. Concept 9.2
  2. Fold Recognition at CASP
  3. CASP4 Threading Servers and Creators
  4. Fold Recognition Meta Servers are Winners

9.3. Progress at CASP

9.4. Early ab initio Prediction

  1. Progress at CASP. Concept 9.3
  2. Progress at CASP
  3. Explanation of Scoring index
  4. Best Results at CASP1 to CASP4
  5. Measuring Target Difficulty
  6. CASP Progress
  1. Early ab initio Prediction. Concept 9.4
  2. Ab initio Early History
  3. Early History
  4. Coordinate and Distance Deviation
  5. Folding as a Random Walk
  6. Wide Distribution of Folds
  7. Very Simple Lattice Model
  8. Potential Energy in torsion Space0
  9. Folding With Restraints1
  10. Folding With Restraints2
  11. Diversity of Folds

9.5. Modern New Fold Prediction

9.6. Winning NF Methods at CASP

  1. Modern New Fold Prediction. Concept 9.5
  2. Modern New Fold Prediction
  3. A Paradigm for Predicting Structure
  4. Energy Vs Rms Cartoons
  5. Energy Vs Rms Reality
  6. Energy Vs Rms
  7. Hierarchical Structure Prediction
  8. Getting an average Model
  9. Hierarchical Prediction Does Well
  10. Folding Energy Functions
  11. Potential Energy in torsion Space
  12. Energy Minimization Folds the Chain
  13. Cooperative Hydrophobic Packing
  14. Cooperative Hydrogen Bonds1
  15. Cooperative Hydrogen Bonds2
  16. Minimization Gives Good Folds
  1. Winning NF Methods at CASP. Concept 9.6
  2. CASP4 New Fold Winners
  3. Winning NF Methods at CASP4
  4. Segment Exchange Monte Carlo
  5. Fragment insertion Monte Carlo
  6. New Potential Improves Recognition
  7. Lattice Monte Carlo
  8. Complicated Lattice
  9. Structure Prediction by Minimization
  10. All-Beta Prediction Success
  11. Segment Folding Monte Carlo
  12. Segment Folding Prediction
  13. CASP5 New Fold Winners
  14. Winning NF Methods at CASP5
  15. Baker at CASP51
  16. Baker at CASP52
  17. Shortle at CASP5
  18. CASP5 Lessons
  19. CASP Summary