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Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction
- 1st Edition - October 4, 2012
- Editor: Irena Roterman-Konieczna
- Language: English
- Paperback ISBN:9 7 8 - 0 - 0 8 - 1 0 1 6 7 1 - 8
- Hardback ISBN:9 7 8 - 1 - 9 0 7 5 6 8 - 1 7 - 6
- eBook ISBN:9 7 8 - 1 - 9 0 8 8 1 8 - 2 5 - 6
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… Read more
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Request a sales quote- 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
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
- No. of pages: 240
- Language: English
- Edition: 1
- Published: October 4, 2012
- Imprint: Woodhead Publishing
- Paperback ISBN: 9780081016718
- Hardback ISBN: 9781907568176
- eBook ISBN: 9781908818256
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