About Book

Bioinformatics has become an important part of many areas of biology. It is the application of computer technology to the management of biological information. In it computers are used to gather, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics and engineering to study and process biological data. Common uses of bioinformatics include the identification of candidate’s genes and single nucleotide polymorphisms (SNPs). In a less formal way, bioinformatics also tries to understand the organizational principles within nucleic acid and protein sequences, called proteomics. The development of efficient algorithms for measuring sequence similarity is an important goal of bioinformatics. This book discusses the recent developments that have taken place in the field of bioinformatics. The various sub-fields of bioinformatics along with technological progress that have future implications are glanced at in this book. It includes data analysis, domain structure prediction, basidiomycetes telomeres, structural bioinformatics, experimental methods, HPV bioinformatics, genetic variants, bioinformatics methodologies and antibody engineering. It brings forth some of the most innovative concepts and elucidates the unexplored aspects of these fields. It includes contribution of experts and scientists which will provide innovative insights to readers. This book will be useful for students, experts and professionals in the fields of molecular biology, genetics and proteomics.

Preface ..................................................................................................................... v

1. Bioinformatics Approach to Screening and Developing Drug against

Ebola ........................................................................................................................ 1

Abstract ........................................................................................................... 1

1. Introduction ................................................................................................... 2

2. Our in silico method ...................................................................................... 6

3. Conclusions .................................................................................................. 11

Acknowledgements ..................................................................................... 11

Conflict of interest ....................................................................................... 11

2. Bioinformatics as a Tool to Identify Infectious Disease Pathogen Peptide

Sequences as Targets for Antibody Engineering .......................................... 18

Abstract ......................................................................................................... 18

1. Introduction ................................................................................................. 18

2. Creating a schematic model ....................................................................... 38

3. Conclusion .................................................................................................... 39

Acknowledgements ..................................................................................... 39

3. Bioinformatics Approaches for Predicting Kinase– Substrate

Relationships ....................................................................................................... 44

Abstract ......................................................................................................... 44

1. Introduction ................................................................................................. 45

2. Comparing prediction tools: data, metrics, and methods .................... 46

3. Beyond the sequence: improving substrate prediction with

contextual information ............................................................................... 50

4. Structural aspects of phosphosites ........................................................... 55

5. The kinase side: determinants of specificity ............................................ 56

6. Conclusions .................................................................................................. 57

4. Application of Bioinformatics Methodologies in the Fields of Skin

Biology and Dermatology ................................................................................. 66

Abstract ......................................................................................................... 66

1. Introduction: both wide angle and focused view of skin biology........ 67

2. Historical perspective ................................................................................. 69

3. Noninvasive sample acquisition ............................................................... 70

4. Epidermal differentiation ........................................................................... 70

5. The skin microbiome ................................................................................... 72

6. UV damage ................................................................................................... 75

7. Skin aging ...................................................................................................... 76

8. Skinomics genome-wide association studies .......................................... 76

9. Transcriptional studies of melanoma ....................................................... 78

10. Wound healing studies ............................................................................... 78

11. Inflammation, cytokines, and chemokines .............................................. 79

12. Psoriasis transcriptome ............................................................................. 79

13. Conclusions .................................................................................................. 82

5. Bioinformatics Approaches to the Functional Profiling of Genetic

Variants ................................................................................................................. 92

1. Introduction ................................................................................................. 92

2. Structural impact of mutations ................................................................ 95

3. Functional impact of mutations ................................................................ 99

4. Mutation prediction: MutPred ................................................................ 104

5. Conclusion .................................................................................................. 108

6. HPV Bioinformatics: In Silico Detection, Drug Design and Prevention

Agent Development ......................................................................................... 115

1. Introduction ............................................................................................... 115

2. In silico HPV related research ................................................................. 116

3. Conclusion .................................................................................................. 131

4. ACknowledgement .................................................................................... 132

7. Applications of Bioinformatics and Experimental Methods to

Intrinsic Disorder-Based Protein-Protein Interactions ............................... 135

1. Introduction ............................................................................................... 135

2. Intrinsically disordered proteins and their structural and

functional studies ...................................................................................... 136

3. Bioinformatics methods for predicting structures of IDPs ................. 145

4. Experimental methods for investigation of IDPs .................................. 153

5. Conclusion .................................................................................................. 160

8. Structural Bioinformatics for Protein Engineering ..................................... 170

1. Introduction ............................................................................................... 170

2. An introduction to molecular dynamics simulations ......................... 172

3. Biotechnological applications .................................................................. 182

4. Trends in structural bioinformatics ....................................................... 196

9. Basidiomycetes Telomeres – A Bioinformatics Approach ....................... 201

1. Introduction ............................................................................................... 201

2. Fungal telomeres - A bioinformatics approach .................................... 206

3. Synteny ....................................................................................................... 225

4. Conclusion .................................................................................................. 229

5. Acknowledgements ................................................................................... 229

10. Bioinformatics Domain Structure Prediction and Homology

Modeling of Human Ryanodine Receptor 2 ............................................... 244

1. Introduction ............................................................................................... 244

2. Physiological function of RyR2 ............................................................... 245

3. Structure of ryanodine receptors ............................................................ 253

4. Cloning, expression and characterization of predicted N-terminal hRyR2

domains ....................................................................................................... 261

5. Conclusion .................................................................................................. 268

6. Acknowledgment ...................................................................................... 269

11. Family Based Studies in Complex Disorders: The Use of Bioinformatics ...

Software for Data Analysis in Studies on Osteoporosis ........................... 282

1. Introduction ............................................................................................... 282

2. Materials and methods ............................................................................. 289

3. Results ......................................................................................................... 297

4. Conclusion .................................................................................................. 307

5. Acknowledgements ................................................................................... 307

Citation ................................................................................................................ 315

Index .................................................................................................................... 317

About Author

Maison Hoppe received his Ph.D. Degree in Biotechnology. He is a Biotechnologist with a strong background in computational biology and bioinformatics at Kosova. His current research activities include protein-protein interaction prediction, gene expression analysis and protein sequence analysis in the field of bioinformatics. Hoppe has authored a number of articles, journal papers, scientific papers and book chapters on proteomics and bioinformatics. He holds prominent memberships of international associations and has been an active participant at international conferences and forums.