ALL LECTURES
Introduction Molecular Architecture I Molecular Architecture II Molecular Simulation I Molecular Simulation II Bioinformatics I Bioinformatics II Prediction I Prediction II

CONCEPTS IN THIS LECTURE
Prediction II
Fold Recognition Fold Recognition at CASP Progress at CASP Early ab initio Prediction Modern New Fold Prediction Winning NF Methods at CASP

9. Prediction II
9.1. Fold Recognition	9.2. Fold Recognition at CASP
SB228 Lecture 9 Lecture9 Structure Prediction II Fold Recognition. Concept 9.1 Fold Recognition Comparative Modeling vs Threading Threading Covers More of Protein Space What is Fold Recognition What is Threading Simple Example A Different Threading Gaps in Threading Frozen approximation Use a Sequence Profile Profile Matching1 Profile Matching2 Deletions Using Structure Insertions Using Structure Getting Good alignments Summary	Fold Recognition at CASP. Concept 9.2 Fold Recognition at CASP CASP4 Threading Servers and Creators Fold Recognition Meta Servers are Winners
9.3. Progress at CASP	9.4. Early ab initio Prediction
Progress at CASP. Concept 9.3 Progress at CASP Explanation of Scoring index Best Results at CASP1 to CASP4 Measuring Target Difficulty CASP Progress	Early ab initio Prediction. Concept 9.4 Ab initio Early History Early History Coordinate and Distance Deviation Folding as a Random Walk Wide Distribution of Folds Very Simple Lattice Model Potential Energy in torsion Space0 Folding With Restraints1 Folding With Restraints2 Diversity of Folds
9.5. Modern New Fold Prediction	9.6. Winning NF Methods at CASP
Modern New Fold Prediction. Concept 9.5 Modern New Fold Prediction A Paradigm for Predicting Structure Energy Vs Rms Cartoons Energy Vs Rms Reality Energy Vs Rms Hierarchical Structure Prediction Getting an average Model Hierarchical Prediction Does Well Folding Energy Functions Potential Energy in torsion Space Energy Minimization Folds the Chain Cooperative Hydrophobic Packing Cooperative Hydrogen Bonds1 Cooperative Hydrogen Bonds2 Minimization Gives Good Folds	Winning NF Methods at CASP. Concept 9.6 CASP4 New Fold Winners Winning NF Methods at CASP4 Segment Exchange Monte Carlo Fragment insertion Monte Carlo New Potential Improves Recognition Lattice Monte Carlo Complicated Lattice Structure Prediction by Minimization All-Beta Prediction Success Segment Folding Monte Carlo Segment Folding Prediction CASP5 New Fold Winners Winning NF Methods at CASP5 Baker at CASP51 Baker at CASP52 Shortle at CASP5 CASP5 Lessons CASP Summary