Genetic Algorithms and Protein Folding

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 References Evolutionary Computation Evolutionary Computation is, like neural networks, an example par excellence for an information processing paradigm that was originally developed and exhibited by nature and later discovered by man who subsequently transformed the general principle into computational algorithms to be put to work on computers. Nature makes in an impressive way use of the principle of geneti