Genetic Algorithms and Protein Folding

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Table of Contents

1 Evolutionary Computation (introduction)

1.1 Methodology

1.1.1 Genetic Algorithms
1.1.2 Evolution Strategy

1.2 Applications

1.2.1 Protein Folding Simulation by Force Field Optimisation

1.2.1.1 Representation Formalism
1.2.1.2 Fitness Function
1.2.1.3 Conformational Energy
1.2.1.4 Genetic Operators
1.2.1.5 Ab initio Prediction Results
1.2.1.6 Side Chain Placement

1.2.2 Multi-Criteria Optimisation of Protein Conformations

1.2.2.1 Vector Fitness Function
1.2.2.2 Specialised Genetic Operators
1.2.2.3 Results

Exercises