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

CONCEPTS IN THIS LECTURE

Prediction I

  1. Why Predict Structure
  2. Knowledge-Based Physics
  3. CASP
  4. Predict Secondary Structure
  5. Sidechain Prediction
  6. Homology Modeling

8. Prediction I

8.1. Why Predict Structure

8.2. Knowledge-Based Physics

  1. SB228 Lecture 8 Lecture8
  2. Structure Prediction I
  3. Why Predict Structure. Concept 8.1
  4. Human Genome
  5. Half of Proteins Are Novel
  6. Is There a Finite Number of Folds
  7. Chothias 1,000 Fold Hypothesis1
  8. Chothias 1,000 Fold Hypothesis2
  1. Knowledge-Based Physics. Concept 8.2
  2. Knowledge-Based Physics
  3. Knowledge-Based Energies1
  4. Environmental Energies
  5. Pair-Wise Energies
  6. Knowledge-Based Geometry
  7. Fragment Libraries
  8. Fit and Complexity
  9. Knowledge-Based Simulation

8.3. CASP

8.4. Predict Secondary Structure

  1. CASP. Concept 8.3
  2. What is CASP
  3. CASP Targets
  4. The CASP Process
  5. CASP Statistics
  6. Hubbard Plots
  7. GDT-TT Score
  8. Assessment
  9. CASP2 Experiences
  10. Simple Z-Score Sum
  11. Which Targets are Which
  1. Predict Secondary Structure. Concept 8.4
  2. Predict Secondary Structure
  3. Predicting Secondary Structure
  4. Secondary Structure States
  5. Early History2
  6. Chou-Fasman Secondary Structure
  7. Early Blind Experiment
  8. Statistical Preferences
  9. Amino Acid Classification
  10. Elementary Neural Network
  11. Training a Neural Network
  12. Sequence Profile
  13. Rost 1993 Neural Network
  14. Jones 1999 Neural Network
  15. Secondary Structure Prediction Quality
  16. Historical Record of Best Predictions At CASP

8.5. Sidechain Prediction

8.6. Homology Modeling

  1. Sidechain Prediction. Concept 8.5
  2. Side Chain Modeling
  3. Basic Idea1
  4. Basic Idea2
  5. Basic Idea3
  6. Simulated Annealing
  7. Segment Match Modeling
  8. Mean Field1
  9. Mean Field2
  10. Generalized Self-Consistent Mean-Field1
  11. Generalized Self-Consistent Mean-Field2
  12. Some Other Methods
  1. Homology Modeling. Concept 8.6
  2. What is Homology Modeling
  3. Loop Methods Are Varied
  4. A Multiple Sequence Alignment
  5. Fssp Structural Alignments2
  6. Servers and Meta Servers
  7. Comparative Modeling Servers and Creators
  8. Meta Servers Are Winners