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Protein Folding in Silico. Woodhead Publishing Series in Biomedicine
Description:
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.
- Discusses a range of ab initio models for protein structure prediction
- Introduces a unique model based on experimental observations
- Describes various methods for the quantitative assessment of the presented models from the viewpoint of
information theory
Contents:
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 â?ofuzzy oil dropâ? 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
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