Protein Folding in Silico

Dedication List of figures List of tables About the editor List of contributors Introduction Chapter 1: The early-stage intermediate Abstract 1.1 Geometric model 1.2 Structural alphabet 1.3 Contingency table 1.4 In search of structural similarities Chapter 2: The late-stage intermediate Abstract: 2.1 The " fuzzy oil drop model 2.2 Quantitative description of the hydrophobic core 2.3 Protein characteristics with respect to the hydrophobic core 2.4 Simulation of late-stage folding Chapter 3: Structural information involved in the interpretation of the stepwise protein folding process Abstract: 3.1 Balancing the quantity of information in the amino acid sequence and the early-stage intermediate 3.2 Zones on the Ramachandran map Chapter 4: The divergence entropy characterizing the internal force field in proteins Abstract: 4.1 Internal force field for nonbonding interactions 4.2 The impact of ligands 4.3 Structures of homodimers - protein-protein interaction 4.4 Protein containing a catalytic center 4.5 The role of exons 4.6 Conclusions Chapter 5: Ligand-binding-site recognition Abstract: 5.1 General model 5.2 ROC curves 5.3 Summary Chapter 6: Use of the âEURoefuzzy oil dropâEUR model to identify the complexation area in protein homodimers Abstract: 6.1 General description 6.2 ROC curves 6.3 Conclusions Chapter 7: Simulation of the polypeptide chain folding process using the "fuzzy oil drop" model Abstract: 7.1 Simulation of the folding process in the presence of an external hydrophobic force field 7.2 Folding in the presence of a ligand 7.3 Influence of external factors on polypeptide chain folding Chapter 8: Misfolded proteins Abstract: 8.1 Introduction 8.2 In silico experiment 8.3 Conclusions 8.4 Appendix 1: details of the molecular dynamics simulation 8.5 Appendix 2: details of the cluster analysis Chapter 9: A Short description of other selected ab initio methods for protein structure prediction Abstract: 9.1 Introduction 9.2 Simplifying the geometric model and the field function 9.3 Lattice model 9.4 ROSETTA 9.5 In search of a global minimum - force field deformation Chapter 10: Conclusion Abstract: 10.1 Acknowledgements Index