Thesis
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Sean Forman
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Thesis in Postscript Form
(10-15 MB)
Abstract
Defense Presentation
TORSION ANGLE SELECTION AND EMERGENT NON-LOCAL SECONDARY STRUCTURE IN PROTEIN STRUCTURE PREDICTION
Why We Care
Post-genome Life Sciences
Outline of Our Approach
Protein and Protein Folding Background
Protein and Amino Acid Structure
Covalent Bonding
Torsion Angles
Secondary Structure
Hydrophobicity
Protein Energetics
Energy Minimization
Current Protein Folding Techniques
Comparative Modeling
Fold Recognition
Ab Initio
Techniques
Overview of Techniques
Overview of HOPS
General Structure of HOPS
Geometry
Energetics
Search
PEX
Algorithms for Torsion Angle Selection
Introduction
Hierarchical Techniques
Optimization Techniques
Ramachandran Plots
Hierarchical Clustering of Torsion Angles
Clustering and Facilities Location
Single Facility Location
Multiple Facility Location
Implementation
Incremental Addition of Cluster Points
Results
Tweaking Algorithms for
-Strand Alignment
Homogeneous Coordinate Systems
Tweaking
Formulation of the Tweaking Problem
Solution of the Tweaking Problem
Termination Criteria
Implementation Details for Tweaking
Tweaking and Nagging
Clustering Results
Test Proteins
Some Clustering Results
Full Results
Incremental Addition of Points
Recommendations
Tweaking Results
Mis-aligned and Re-aligned Proteins
Tweaking Opportunity
Predicted Structures with Sheets
Discussion and Future Work
Evaluation of HOPS
Future Direction in Our Work
Future Directions in the Field
Amino Acids
Protein Data Bank Format
Ramachandran Plots
Torsion Angle Errors for protein G Prediction
Bibliography
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sforman@sju.edu
-Strand Alignment