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Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction
Irena Roterman-Konieczna (Edited by)
9781907568176, Elsevier Science
Hardback, published 4 October 2012
240 pages
23.4 x 15.6 x 2.1 cm, 0.5 kg
Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks.
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 “fuzzy oil drop†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
Subject Areas: Biochemistry [PSB]
