Protein Folding in Silico

Protein Folding in Silico

Protein Folding Versus Protein Structure Prediction

1st Edition - October 4, 2012

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  • Editor: Irena Roterman-Konieczna
  • eBook ISBN: 9781908818256
  • Hardcover ISBN: 9781907568176

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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

  • Dedication

    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

    Chapter 8: Misfolded proteins


    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


    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


    10.1 Acknowledgements


Product details

  • No. of pages: 240
  • Language: English
  • Copyright: © Woodhead Publishing 2012
  • Published: October 4, 2012
  • Imprint: Woodhead Publishing
  • eBook ISBN: 9781908818256
  • Hardcover ISBN: 9781907568176

About the Editor

Irena Roterman-Konieczna

Professor Irena Roterman-Konieczna her 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. She is the Chief Editor of the journal Bio-Algorithms and Med-Systems (de Gruyter).

Affiliations and Expertise

Professor of Bioinformatics, Jagiellonian University, Poland

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