Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction
- 1st Edition - October 4, 2012
- Latest edition
- 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
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
Those in the bio-sciences field: biochemistry, biotechnology, computer aided drug design, medical biochemistry and bioinformatics
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
- Edition: 1
- Latest edition
- Published: October 4, 2012
- Language: English
IR
Irena Roterman-Konieczna
Professor Irena Roterman-Konieczna completed her PhD at the Nicolaus Copernicus Medical Academy Krakow, Poland and undertook her postdoctoral studies at Cornell University, USA. She is the director of the Department of Bioinformatics and Telemedicine at Jagiellonian University – Medical College, Poland. Her fields of interest are protein structure, folding simulation as well as systems biology. She is the author of "Protein Folding in Silico", published by Woodhead Publishing in 2012., and "From Globular Proteins to Amyloids" published by Elsevier in 2020. She is the Chief Editor of the journal Bio-Algorithms and Med-Systems (de Gruyter).
Affiliations and expertise
Professor of Bioinformatics, Jagiellonian University, PolandRead Protein Folding in Silico on ScienceDirect