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Computational Molecular Biology An Introduction - Peter Clote, Rolf Backofen

Contents


Molecular Biology
1
1.1 Some Organic Chemistry 3
1.2 Small Molecules 4
1.3 Sugars 6
1.4 Nucleic Acids 6
1.4.1 Nucleotides 6
1.4.2 DNA 8
1.4.3 RNA 13
1.5 Proteins 14
1.5.1 Amino Acids 14
1.5.2 Protein Structure 15
1.6 From DNA to Proteins 17
1.6.1 Amino Acids and Proteins 17
1.6.2 Transcription and Translation 19
1.7 Exercises 21
Acknowledgements and References 22

2
Math Primer
23
2.1 Probability 23
2.1.1 Random Variables 25
2.1.2 Some Important Probability Distributions 27
2.1.3 Markov Chains 38
2.1.4 Metropolis–Hastings Algorithm 43

2.1.5 Markov Random Fields and Gibbs Sampler 47
2.1.6 Maximum Likelihood 52
2.2 Combinatorial Optimization 53
2.2.1 Lagrange Multipliers 53
2.2.2 Gradient Descent 54
2.2.3 Heuristics Related to Simulated Annealing 54
2.2.4 Applications of Monte Carlo 55
2.2.5 Genetic Algorithms 60
2.3 Entropy and Applications to Molecular Biology 61
2.3.1 Information Theoretic Entropy 62
2.3.2 Shannon Implies Boltzmann 63

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