Computation in BioInformatics

COMPUTATION IN BIOINFORMATICS

Bioinformatics is a platform between the biology and information technology and this book provides readers with an understanding of the use of bioinformatics tools in new drug design.

The discovery of new solutions to pandemics is facilitated through the use of promising bioinformatics techniques and integrated approaches. This book covers a broad spectrum of the bioinformatics field, starting with the basic principles, concepts, and application areas. Also covered is the role of bioinformatics in drug design and discovery, including aspects of molecular modeling. Some of the chapters provide detailed information on bioinformatics related topics, such as silicon design, protein modeling, DNA microarray analysis, DNA-RNA barcoding, and gene sequencing, all of which are currently needed in the industry. Also included are specialized topics, such as bioinformatics in cancer detection, genomics, and proteomics. Moreover, a few chapters explain highly advanced topics, like machine learning and covalent approaches to drug design and discovery, all of which are significant in pharma and biotech research and development.

Audience

Researchers and engineers in computation biology, information technology, bioinformatics, drug design, biotechnology, pharmaceutical sciences.

Auteur

S. Balamurugan, PhD is the Director of Research and Development, Intelligent Research Consultancy Services (iRCS), Coimbatore, Tamilnadu, India. His PhD is in Information Technology, and he has published 45 books, 200+ international journals/conferences, and 35 patents.

Anand Krishnan, PhD is the NRF-DSI Innovation Fellow, Department of Chemical Pathology, University of the Free State (Bloemfontein Campus), Bloemfontein, South Africa. His expertise is in organic chemistry/medical biochemistry/integrative medicine/nano(bio)technology/drug discovery. Dinesh Goyal, PhD is the Director at the Poornima Institute of Engineering and Technology, Jaipur, India. His research interests are related to information & network security, image processing, data analytics, and cloud computing. Balakumar Chandrasekaran, PhD is an assistant professor at the Faculty of Pharmacy, Philadelphia University, Jordan. He has published many research articles and book chapters as well as two patents. Boomi Pandi, PhD is an assistant professor in the Department of Bioinformatics, Alagappa University, Karaikudi, India. He has a number of international articles to his credit. Among his research interest are nanomaterials and polymer synthesis, bio-inorganic chemistry, and nano-drug delivery.

Texte du rabat
Bioinformatics is a platform between the biology and information technology and this book provides readers with an understanding of the use of bioinformatics tools in new drug design.

The discovery of new solutions to pandemics is facilitated through the use of promising bioinformatics techniques and integrated approaches. This book covers a broad spectrum of the bioinformatics field, starting with the basic principles, concepts, and application areas. Also covered is the role of bioinformatics in drug design and discovery, including aspects of molecular modeling. Some of the chapters provide detailed information on bioinformatics related topics, such as silicon design, protein modeling, DNA microarray analysis, DNA-RNA barcoding, and gene sequencing, all of which are currently needed in the industry. Also included are specialized topics, such as bioinformatics in cancer detection, genomics, and proteomics. Moreover, a few chapters explain highly advanced topics, like machine learning and covalent approaches to drug design and discovery, all of which are significant in pharma and biotech research and development. Audience Researchers and engineers in computation biology, information technology, bioinformatics, drug design, biotechnology, pharmaceutical sciences.

Résumé
COMPUTATION IN BIOINFORMATICS Bioinformatics is a platform between the biology and information technology and this book provides readers with an understanding of the use of bioinformatics tools in new drug design. The discovery of new solutions to pandemics is facilitated through the use of promising bioinformatics techniques and integrated approaches. This book covers a broad spectrum of the bioinformatics field, starting with the basic principles, concepts, and application areas. Also covered is the role of bioinformatics in drug design and discovery, including aspects of molecular modeling. Some of the chapters provide detailed information on bioinformatics related topics, such as silicon design, protein modeling, DNA microarray analysis, DNA-RNA barcoding, and gene sequencing, all of which are currently needed in the industry. Also included are specialized topics, such as bioinformatics in cancer detection, genomics, and proteomics. Moreover, a few chapters explain highly advanced topics, like machine learning and covalent approaches to drug design and discovery, all of which are significant in pharma and biotech research and development. Audience Researchers and engineers in computation biology, information technology, bioinformatics, drug design, biotechnology, pharmaceutical sciences.

Contenu
Preface xiii

1 Bioinfomatics as a Tool in Drug Designing 1
*Rene Barbie Browne, Shiny C. Thomas and Jayanti Datta Roy*

1.1 Introduction 1

1.2 Steps Involved in Drug Designing 3

1.2.1 Identification of the Target Protein/Enzyme 5

1.2.2 Detection of Molecular Site (Active Site) in the Target Protein 6

1.2.3 Molecular Modeling 6

1.2.4 Virtual Screening 9

1.2.5 Molecular Docking 10

1.2.6 QSAR (Quantitative Structure-Activity Relationship) 12

1.2.7 Pharmacophore Modeling 14

1.2.8 Solubility of Molecule 14

1.2.9 Molecular Dynamic Simulation 14

1.2.10 ADME Prediction 15

1.3 Various Softwares Used in the Steps of Drug Designing 16

1.4 Applications 18

1.5 Conclusion 20

References 20

2 New Strategies in Drug Discovery 25
*Vivek Chavda, Yogita Thalkari and Swati Marwadi*

2.1 Introduction 26

2.2 Road Toward Advancement 27

2.3 Methodology 30

2.3.1 Target Identification 30

2.3.2 Docking-Based Virtual Screening 32

2.3.3 Conformation Sampling 33

2.3.4 Scoring Function 34

2.3.5 Molecular Similarity Methods 35

2.3.6 Virtual Library Construction 37

2.3.7 Sequence-Based Drug Design 37

2.4 Role of OMICS Technology 38

2.5 High-Throughput Screening and Its Tools 40

2.6 Chemoinformatic 44

2.6.1 Exploratory Data Analysis 45

2.6.2 Example Discovery 46

2.6.3 Pattern Explanation 46

2.6.4 New Technologies 46

2.7 Concluding Remarks and Future Prospects 46

References 48

3 Role of Bioinformatics in Early Drug Discovery: An Overview and Perspective 49
*Shasank S. Swain and Tahziba Hussain*

3.1 Introduction 50

3.2 Bioinformatics and Drug Discovery 51

3.2.1 Structure-Based Drug Design (SBDD) 52

3.2.2 Ligand-Based Drug Design (LBDD) 53

3.3 Bioinformatics Tools in Early Drug Discovery 54

3.3.1 Possible Biological Activity Prediction Tools 55

3.3.2 Possible Physicochemical and Drug-Likeness Properties Verification Tools 58

3.3.3 Possible Toxicity and ADME/T Profile Prediction Tools 60

3.4 Future Directions With Bioinformatics Tool 61

3.5 Conclusion 63

Acknowledgements 64

References 64

4 Role of Data Mining in Bioinformatics 69
*Vivek P. Chavda, Amit Sorathiya, Disha Valu and Swati Marwadi*

4.1 Introduction 70

4.2 Data Mining Methods/Techniques 71

4.2.1 Classification 71

4.2.1.1 Statistical Techniques 71

4.2.1.2 Clustering Technique 73

4.2.1.3 Visualization 74

4.2.1.4 Induction Decision Tree Technique 74

4.2.1.5 Neural Network 75

4.2.1.6 Association Rule Technique 75

4.2.1.7 Classification 75

4.3 DNA Data Analysis 77

4.4 RNA Data Analysis…