Polarity Index In Proteins - A Bioinformatics Tool

By Carlos Polanco

Polarity is a physico-chemical property that characterizes the electromagnetic stability of a protein and can be used to predict its plausible pathogenic action. For this reason, polarity is regarded as a major factor in most mathematical-computational algorithms that seek to characterize peptides and proteins. The Polarity Index Method makes it possible to reproduce the main classification of peptide proteins found in different databases, with a high degree of discriminative efficiency.
Polarity Index In Proteins is a brief monograph that explains the foundations of the polarity index method and presents examples of the application of this method for identifying the structural and functional relationships of different types of proteins (including cell penetrating peptides and natively unfolded proteins).
The monograph is divided into sections that cover basic protein biochemistry, the computational mathematical foundations of the polarity index method, the application of the method on different protein structures, and the evaluation of the results of famous experiments on biogenesis (Miller & Urey, Fox & Harada, Rode) by the same method.
Polarity Index In Proteins serves as an essential handbook for students and researchers in the field of bioinformatics, proteomics as well as for studies on the role of proteins in the origin of life.

• Language: English
• Publisher: Bentham Science Publishers
• Release date: Jun 29, 2016
• ISBN: 9781681082691

Book preview

Table of Contents

Welcome

Table of Contents

Title Page

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Disclaimer:

Limitation of Liability:

General:

FOREWORD

PREFACE

CONFLICT OF INTEREST

ACKNOWLEDGEMENTS

Acronyms

Part I-PRELIMINARIES

Macromolecules

Abstract

1.1. The Living and Non-living Entities

1.2. Proteins

1.2.1. Primary Structure

1.2.2. Secondary Structure

1.2.3 . Tertiary Structure

1.2.4. Quaternary Structure

1.2.5. Conformational Changes

1.3. The Water

1.4. Considerations

References

Electromagnetic Stability

Abstract

2.1. Ionization Energy

2.2. Chemical Bonds

2.2.1. Covalent Bond

2.2.2. Non-covalent Bonds

2.3. Considerations

References

Part II-FOUNDATIONS

Polarity Index Method

Abstract

3.1. Supervised Algorithms

3.2. Quantitative Structure Activity Relationship Models

3.2.1. Advantages

3.2.2. Disadvantages

3.2.3. Minimizing Risk

3.3. Polarity Index Method

3.3.1. Matrices ∑ni=1 Qi and Qi

3.3.2. Matrix

3.3.3. Weighting

3.3.4. Comparison

3.4. Considerations

References

Mathematical Foundation

Abstract

4.1. Smooth Curves

4.1.1. Critical Points

4.2. Singularities and Regularities

4.3. Catastrophic Bifurcation Points

4.4. Matrix

4.5. Considerations

References

Computational Implementation

Abstract

5.1. Types of Processing

5.2. Microprocessing

5.3. Aims & Focus

5.4. Considerations

References

Pathogenic Bacteria

Abstract

6.1. Functionality

6.2. Current Taxonomy

6.3. Bacteria

6.3.1. Gram + Bacteria

Bioinformatics Test

6.3.2. Gram – Bacteria

Bioinformatics Test

6.3.3. Selective Cationic Amphipatic Antibacterial Peptides

Bioinformatics Test

6.3.4. Tuberculosis

Bioinformatics Test

6.4. Viruses

Bioinformatics test

6.5. Fungi

Bioinformatics Test

6.6. Cancer Cells

Bioinformatics Test

6.7. Similarities and Differences

6.8. Special Notes

6.9. Considerations

References

Part III-STRUCTURAL PROPERTIES

Cell Penetrating Peptides

Abstract

7.1. Description

7.1.1. Non Endocytic Pathway

Bioinformatics Test

7.1.2. Endocytic Pathway

Bioinformatics Test

7.1.3. Unknown Pathway

7.1.4. SCAAP–CPP

Bioinformatics Test

7.2. Similarities and Differences

7.3. Special Notes

7.4. Considerations

References

Amyloid Proteins

Abstract

8.1. Protein Folding

8.2. Polar Profile

8.3. Lipoproteins

Bioinformatics Test

8.4. Natively Unfolded Proteins

Bioinformatics Test

8.5. Partially Folded Proteins

Bioinformatics Test

8.6. Natively Folded Proteins

Bioinformatics Test

8.7. Neurons Proteins

Bioinformatics Test

8.8. Similarities and Differences

8.9. Special Notes

8.10. Considerations

References

Globular & Fibrous Proteins

Abstract

9.1. Preliminaries

9.2. Globular Proteins

Bioinformatics Test

9.3. Fibrous proteins

Bioinformatics Test

9.4. Similarities and Differences

9.5. Special notes

9.6. Considerations

References

Part IV-BIOGENESIS & TRENDS

Biogenetic Experiments

Abstract

10.1. Biogenesis

10.2. Miller & Urey: Primordial Soup

Bioinformatics Test

10.3. Fox & Harada: Proteinoids

Bioinformatics Test

10.4 . Rode: Dipeptides

Bioinformatics Test

10.5. Similarities and Differences

10.6. Considerations

References

Future Directions

Abstract

11.1. Proteomics Trends

11.2. Distributed Computing

11.3. Synthetic Proteins

11.4. Bioinformatics

11.5. Considerations

References

Appendix A-Computational Tools

A.1. Preliminaries

A.2. Preparation Files

A.3. Polarity Index Method Program

A.4. Output Datasets

Appendix B-Protein Databases

B.1. APD2 Database

B.2. AMYPdb Database

B.3. Uniprot Database

B.4. CPPsite Database

B.5. SCAAP Dataset

B.6. Amyloidosis Datasets

B.7. Considerations

References

GLOSSARY

References

Polarity Index in Proteins–

A Bioinformatics Tool

Authored By:

Carlos Polanco

Faculty of Sciences

Universidad Nacional Autónoma de México

México

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