Advances in Protein Chemistry and Structural Biology

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