ALL LECTURES
Introduction
Molecular Architecture I
Molecular Architecture II
Molecular Simulation I
Molecular Simulation II
Bioinformatics I
Bioinformatics II
Prediction I
CONCEPTS IN THIS LECTURE
Prediction I
Why Predict Structure
Knowledge-Based Physics
CASP
Predict Secondary Structure
Sidechain Prediction
Homology Modeling
8. Prediction I
8.1. Why Predict Structure
8.2. Knowledge-Based Physics
SB228 Lecture 8 Lecture8
Structure Prediction I
Why Predict Structure. Concept 8.1
Human Genome
Half of Proteins Are Novel
Is There a Finite Number of Folds
Chothias 1,000 Fold Hypothesis1
Chothias 1,000 Fold Hypothesis2
Knowledge-Based Physics. Concept 8.2
Knowledge-Based Physics
Knowledge-Based Energies1
Environmental Energies
Pair-Wise Energies
Knowledge-Based Geometry
Fragment Libraries
Fit and Complexity
Knowledge-Based Simulation
8.3. CASP
8.4. Predict Secondary Structure
CASP. Concept 8.3
What is CASP
CASP Targets
The CASP Process
CASP Statistics
Hubbard Plots
GDT-TT Score
Assessment
CASP2 Experiences
Simple Z-Score Sum
Which Targets are Which
Predict Secondary Structure. Concept 8.4
Predict Secondary Structure
Predicting Secondary Structure
Secondary Structure States
Early History2
Chou-Fasman Secondary Structure
Early Blind Experiment
Statistical Preferences
Amino Acid Classification
Elementary Neural Network
Training a Neural Network
Sequence Profile
Rost 1993 Neural Network
Jones 1999 Neural Network
Secondary Structure Prediction Quality
Historical Record of Best Predictions At CASP
8.5. Sidechain Prediction
8.6. Homology Modeling
Sidechain Prediction. Concept 8.5
Side Chain Modeling
Basic Idea1
Basic Idea2
Basic Idea3
Simulated Annealing
Segment Match Modeling
Mean Field1
Mean Field2
Generalized Self-Consistent Mean-Field1
Generalized Self-Consistent Mean-Field2
Some Other Methods
Homology Modeling. Concept 8.6
What is Homology Modeling
Loop Methods Are Varied
A Multiple Sequence Alignment
Fssp Structural Alignments2
Servers and Meta Servers
Comparative Modeling Servers and Creators
Meta Servers Are Winners