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Advances in Protein Chemistry and Structural Biology - 1st Edition - ISBN: 9780128001684, 9780128003732

Advances in Protein Chemistry and Structural Biology, Volume 94

1st Edition

Serial Editor: Rossen Donev
Hardcover ISBN: 9780128001684
eBook ISBN: 9780128003732
Imprint: Academic Press
Published Date: 27th March 2014
Page Count: 488
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Table of Contents

Chapter One: Bioinformatics Tools to Identify and Quantify Proteins Using Mass Spectrometry Data

1 Introduction

2 MS Data

3 Protein Identification

4 Protein Quantification

5 Conclusion


Chapter Two: Unraveling Oxidation-Induced Modifications in Proteins by Proteomics

1 A Very Brief Introduction to Oxidative Stress and Redox Homeostasis

2 Proteins as Targets of Oxidative Modification

3 Redox Proteomics: The Comprehensive Study of Oxidation-Induced Protein Damage

4 The Use of Proteomics for Mapping the Redox Homeostasis Network: Lessons from Cancer Research

5 Perspectives and Conclusions

Chapter Three: Role of Proteomics in Biomarker Discovery: Prognosis and Diagnosis of Neuropsychiatric Disorders

1 Summary

2 Commonly Used Methods for Proteome Characterization

3 Proteomics and Biomarker

4 Diagnosis of Neuropsychiatric Disorders

5 Proteomics of Neuropsychiatric Disorders

6 Strength, Weakness, and Future Challenges: Biomarker Discovery

7 Concluding Remarks

Chapter Four: On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions

1 Introduction

2 Knowledge-Based Potentials

3 Modeling of Protein Interactions Using Templates

4 Modeling Interactions of Proteins Using Docking

5 Prediction of Protein-Binding Regions

6 Characterization of Transcription Factor-Binding Sites

7 Adapting Split-Statistical Potentials for Protein–DNA Interactions

8 Conclusions


Chapter Five: Algorithms, Applications, and Challenges of Protein Structure Alignment

1 Introduction

2 Structural Alphabet

3 Protein Pairwise Structure Alignment

4 Protein MSA

5 Conclusions and Perspectives

Chapter Six: Application of Evolutionary Based in Silico Methods to Predict the Impact of Single Amino Acid Substitutions in Vitelliform Macular Dystrophy

1 Introduction

2 Materials and Methods

3 Results

4 Discussion

5 Conclusion


Chapter Seven: Current State-of-the-Art Molecular Dynamics Methods and Applications

1 Introduction

2 The Role of Computer Experiments in Modern Science

3 Brief History of Computer Molecular Simulations

4 Physics in MD

5 Algorithms for MD Simulations

6 Computational Complexity of MD Simulations and Methods to Increase Efficiency

7 High-Performance Parallel Computing

8 General-Purpose Computing Using Graphics Processing Units

9 Software for MD Simulations

10 Force Fields for MD

11 Current Limitations of MD

12 Conclusions


Chapter Eight: Intrinsically Disordered Proteins—Relation to General Model Expressing the Active Role of the Water Environment

1 Introduction

2 Definition of the Fuzzy Oil Drop Model

3 Results

4 Discussion

5 Conclusions


Chapter Nine: Conformational Elasticity can Facilitate TALE–DNA Recognition

1 Introduction

2 Methods

3 Results

4 Discussion


Chapter Ten: Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research

1 Introduction

2 Computational Methods in SAP Analysis

3 Database Resources for SAPs

4 Molecular Phenotypic Effect Analysis

5 Sequence Information Analysis

6 Computational Methods for Structure Determination

7 Docking

8 Types of Docking

9 Molecular Dynamics

10 Concluding Remarks


Author Index
Subject Index


This eclectic volume features two major topics: applications of mass spectrometry in bioscience; and computational methods for analysis of protein structure and interactions with other macromolecules.

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics.

Key Features

  • Describes advances in application of powerful techniques in a wide bioscience area
  • Chapters are written by authorities in their field
  • Targeted to a wide audience of researchers, specialists, and students
  • The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables


The intended audiences for this volume are researchers and specialists in protein structure and interactions, cancer biology, psychiatry and mass spectrometry. This volume would be also of a great use to students working on projects from the abovementioned areas.


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© Academic Press 2014
27th March 2014
Academic Press
Hardcover ISBN:
eBook ISBN:

Ratings and Reviews

About the Serial Editor

Rossen Donev

Rossen Donev

Rossen Donev received his PhD degree in 1999 from the Institute of Molecular Biology, Bulgarian Academy of Sciences. He did postdoctoral training at Imperial Cancer Research Fund, UK (renamed after the merger with Cancer Research Campaign to Cancer Research UK, London Research Institute) and Cardiff University. In 2007 he was awarded a New Investigator Grant Award from the Medical Research Council (UK) to establish himself as an independent Principle Investigator. In 2010 Dr. Donev was appointed Senior Lecturer at Swansea University. In 2016 Dr. Donev joined MicroPharm Ltd (UK) where currently he is Head of Research. He has published more than 60 research papers, chaired scientific meetings and given invited plenary talks. Rossen Donev has consulted on projects related to development of treatments for neurodevelopmental disorders and cancer therapies. He serves as Editor-in-Chief of the Advances in Protein Chemistry and Structural Biology and on editorial board of several other journals. His research interests include signaling pathways involved in neuropsychiatric disorders and tumor escape from the immune system, and development of therapeutic strategies for their treatment. More recently he has focused on development of immunotherapeutics for non-systemic applications.

Affiliations and Expertise

Swansea University, UK