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.

Key Features

  • 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

Table of Contents


List of figures

List of tables

About the editor

List of contributors


Chapter 1: The early-stage intermediate


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


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


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


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


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


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


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


No. of pages:
© 2012
Woodhead Publishing
Print ISBN:
Electronic ISBN:

About the editor

Irena Roterman-Konieczna

Dr Irena Roterman-Konieczna heads the bioinformatics group at the Jagiellonian University Medical College and the Faculty of Physics, Astronomy and Applied Computer Science. Her background is in theoretical chemistry, and her research focuses on bioinformatics, with specific focus on protein structure prediction.

Affiliations and Expertise

Jagiellonian University Medical College