Advances in Protein Chemistry and Structural Biology, Volume 94

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

1 Introduction

2 MS Data

3 Protein Identification

4 Protein Quantification

5 Conclusion

Acknowledgments

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

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
Abstract

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
Abstract

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

Acknowledgments

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

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
Abstract

1 Introduction

2 Materials and Methods

3 Results

4 Discussion

5 Conclusion

Acknowledgments

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

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

Acknowledgments

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

1 Introduction

2 Definition of the Fuzzy Oil Drop Model

3 Results

4 Discussion

5 Conclusions

Acknowledgments

Chapter Nine: Conformational Elasticity can Facilitate TALE–DNA Recognition
Abstract

1 Introduction

2 Methods

3 Results

4 Discussion

Acknowledgments

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

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

Acknowledgments

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.

• 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.