
Recent Advances in Computer Aided Drug Designing
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Content
- Intro
- Contents
- Foreword
- Preface
- Chapter 1
- Online Drug Data Banks and Molecular Libraries
- Abstract
- 1. Introduction
- 2. Expanse of Drug Databanks
- 3. Commercial Molecular Libraries
- 3.1. Reaxys
- 3.2. SciFinder
- 4. Public Data Aggregators
- 4.1. PubChem
- 4.2. ChEMBL
- 4.3. UniChem
- 4.4. ChemSpider
- 5. Scientific Drug Databanks
- 5.1. KEGG COMPOUND
- 5.2. ZINC
- 6. Natural Products Database
- 6.1. MarinLit
- 6.2. Seaweed Metabolite Database (SWMD)
- Conclusion
- References
- Chapter 2
- Computational Approaches for Drug Screening and Pharmacokinetic Studies
- Abstract
- 1. Introduction
- 2. Drug Likeliness Properties
- 3. Virtual Screening
- 3.1. AutoDock
- 3.2. Dock
- 3.3. Glide
- 3.4. PyRx
- 4. Pharmacokinetics and Drug Designing
- 5. Tools for ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) Screening
- Conclusion
- References
- Chapter 3
- Introduction to Molecular Modelling and Structure Prediction
- Abstract
- 1. Introduction
- 2. Methods Used in Molecular Modelling
- 2.1. Methods for Structure Prediction
- 2.1.1. Template Based Structure Modelling
- 2.1.1.1. Homology Modeling
- 2.1.1.1.1. Identification of Template Structure Related to Target Sequence
- 2.1.1.1.2. Selection of Template Structure
- 2.1.1.1.3. Sequence Alignment to Template Structure
- 2.1.1.1.4. Homology Modelling Based on the Conserved Fragment
- 2.1.1.1.5. Homology Modelling Based on Atomic Coordinates Reconstruction
- 2.1.1.1.6. Homology Modelling by Satisfaction of Spatial Restraints
- 2.1.1.1.7. Homology Modelling via Combining Structures
- 2.1.1.1.8. Homology Modelling with Meta-Servers
- 2.1.1.2. Molecular Threading Approach for Structure Prediction
- 2.1.1.3. Template-Free or de novo Structure Modelling
- 2.1.1.4. Knowledge-Based Structure Prediction and Refinement
- 2.1.1.5. Physics Based Free-Template Modelling
- 2.2. Structure Evaluation
- 2.3. Structure Visualisation
- 3. Application
- 4. Limitation
- Conclusion
- References
- Chapter 4
- Docking and Molecular Dynamics Simulations for Methotrexate Delivery by Graphene
- Abstract
- 1. Introduction
- 2. Computational Methods
- 2.1. Structure
- 2.2. Molecular Docking Simulation
- 2.3. Molecular Dynamics Simulation Methods
- 3. Results and Discussion
- 3.1. Docking
- 3.2. MD Simulation
- Conclusion
- References
- Chapter 5
- In Silico Approach to Study the Effect of Mutation on Protein Stability, Function and Potential Binding of an Inhibitor
- Abstract
- 1. Introduction
- 2. Drug Resistance and Genetic Polymorphism: Personalized Medicines
- 3. In Silico Approach Applying Molecular Docking Coupled to Molecular Dynamic Simulations
- 3.1. Pipeline to Conduct the In Silico Study
- 3.1.1. Databases for Protein Structures and SNPs
- 3.1.2. In Silico Functional Analysis of the Mutations or SNPs Using Prediction Tools
- 3.1.2.1. Functional Characterization of Mutations or SNPs
- 3.1.2.2. Biophysical Characterization of Altered Amino Acid Residue
- 3.1.3. Prediction of Favorable and Stabilizing Mutations
- 3.1.3.1. Variant Protein Stability Prediction
- 3.1.3.2. Stability Centers Identification
- 3.1.4. Protein Flexibility
- 3.1.5. Residue Interaction Profile and Visualization of Residue
- 3.1.6. Ligand-Binding Pockets Prediction
- 3.1.7. Protein-Membrane Interaction Prediction
- 3.1.8. Protein-Protein Interaction Site Prediction
- 3.1.9. Automatic Online Mapping of Variants on 3D Structure
- 3.1.10. Modeling Variants
- 3.1.11. Molecular Docking Analysis and Virtual Screening
- 3.1.12. Molecular Dynamics Simulations
- Conclusion
- Acknowledgments
- References
- Chapter 6
- Methods for Tertiary Structure Prediction of Protein and Qualitative Assessment
- Abstract
- 1. Introduction
- 2. Need for Tertiary Structure Prediction
- 3. Different Approaches to Tertiary Structure Prediction
- 3.1. Ab-Initio Method
- 3.1.1. Steps in Ab-Initio Modeling
- 3.1.2. Initialization of Conformation
- 3.1.3. Conformational Search
- 3.1.4. Prediction of the Native Fold
- 3.1.5. Model Assessment
- 3.1.6. Webtools and Softwares
- 3.2. Threading Approach
- 3.2.1. Web Tools/Software Used for Threading
- 3.3. Homology Modeling
- 3.3.1. Template Identification and Selection
- 3.3.2. Alignment and Its Correction
- 3.3.3. Model Building
- 3.3.4. Model Optimization
- 3.3.5. Model Evaluation
- 4. Method of Evaluation of Model
- Conclusion
- References
- Chapter 7
- Drug Design Utilizing Molecular Docking Based Binding Analyses of Human 5HT-Transporter Inhibitors to Combat Internet Addiction and Gaming Disorders
- Abstract
- 1. Introduction
- 1.1. Internet Addiction and Gaming Disorders
- 1.2. Role of Serotonin and Dopamine Receptor in IAD and IGD
- 1.2.1. Serotonin
- 1.2.2. Dopamine
- 1.3. Mode of Treatment to Combat IAD and IGD
- 1.4. Mode of Action
- 2. Materials and Methods
- 2.1. Data Set
- 2.2. Computational
- 3. Results and Discussion
- Conclusion
- Conflict of Interest
- References
- Chapter 8
- The Significance and Applicability of Computational Approaches in Combating COVID-19
- Abstract
- 1. Introduction
- 2. Genomic and Proteomic Study
- 3. Phylogenetic Analysis
- 4. Computer-Aided Drug Design
- 5. Vaccine Design
- 6. Systems Biology Approach
- 7. Next-Generation Sequencing
- 8. Artificial Intelligence
- Conclusion
- Contribution of Authors
- References
- Chapter 9
- Molecular Docking of NSAIDs to Cyclooxygenase (COX-2)
- Abstract
- 1. Introduction
- 1.1. Cyclooxygenase Isoforms, Structure and Function
- 1.2. COX Isoforms and Functions
- 1.3. Crucial Aspects of COX-2
- 1.4. Molecular Structures of NSAIDS
- 1.5. Chemical Properties of Selective COX-2 Inhibitors
- 2. Materials and Methods
- 2.1. Servers and Software Applied for the Study
- 2.2. Methodology
- 3. Data Collection and Analysis
- 3.1. Query Sequence-(FASTA Format)
- 3.2. The Sequence (.seq) File of Target for Alignment
- 3.3. The Script for Alignment File Is as Follows
- 4. Results
- 4.1. Docking of Analogs with Receptor
- 5. Comparative Analysis
- 6. Discussion and Conclusion
- Acknowledgments
- References
- Chapter 10
- Molecular Dynamics Simulation in Drug Discovery
- Abstract
- 1. Introduction
- 2. Methods of MD Simulation
- 2.1. Force-Fields for MD Simulation
- 2.2. Energy Minimization
- 2.3. Conformational Search Algorithm
- 3. MDS Analysis Parameters
- 3.1. Root Mean Square Deviation (RMSD)
- 3.2. Root Mean Square Fluctuation (RMSF)
- 3.3. Radius of Gyration (Rg)
- 3.4. Hydrogen Bonding
- 3.5. Binding Free Energy Calculation
- 4. Application of MDS
- 4.1. Structural Analysis of Modeled Protein
- 4.2. Dynamics of Protein-Ligand Complex
- 4.3. Binding Dynamics at Other Sites
- 4.4. Protein Folding/Unfolding Dynamics
- 4.5. Impact of Mutation on Structural Stability and Selectivity
- 4.6. MDS Analysis of Nutrients Processing
- Conclusion
- Conflict of Interest
- References
- Chapter 11
- Pharmacogenomics: Current Trends and Future Possibilities
- Abstract
- 1. Introduction
- 1.1. Adverse Drug Reaction
- 2. Variant of Pharmacogenomics Importance
- 3. Pharmacogenes: Genes of Pharmacogenomics Importance
- 4. Current Trends for Mining of Pharmacogenes
- 4.1. Experimental Trends
- 4.2. Bioinformatics Trends
- 4.3. Bioinformatics Data Resources for Pharmacogenomics
- 4.4. PharmGKB
- 4.5. General Purpose Resources
- 5. Population Specific Genomics Projects
- 5.1. Universal Methodologies and Data Formats
- 5.2. Data Sharing
- 5.3. Associations among Consortiums and Projects (Across Countries)
- 6. Use of Pharmacogenomics in Drug Development Process
- 7. Decision Making Process
- 8. Scope and Barriers of Pharmacogenomics
- Conclusion
- References
- Chapter 12
- Artificial Intelligence: Prospects in Drug Discovery and Health Technology
- Abstract
- 1. Introduction
- 2. Basics of AI with Relation to Machine Learning
- 3. Healthcare and Biomedical Data
- 4. AI Paradigms
- 5. AI Techniques: ML and NLP
- 5.1. Classical ML
- 5.1.1. Support Vector Machine
- 5.1.2. Random Forest
- 5.1.3. Neural Networks
- 5.1.4. Deep Learning
- 6. Natural Language Processing
- 7. AI Applications in Drug Discovery and Healthcare
- 7.1. Personalized Treatment
- 7.2. Epidemic Outbreak Prediction
- 7.3. Drug Discovery
- 7.3.1. Target Identification and Validation
- 7.3.2. Small-Molecule Design and Optimization
- 7.3.3. Predictive Biomarkers
- 8. Discussion
- Conclusion
- References
- Chapter 13
- Bioinformatics Intervention in Microbial Therapeutic Enzymes: An Update
- Abstract
- 1. Introduction
- 2. Recombinant DNA Technology of Microbial Therapeutic Enzymes
- 2.1. Isolation of Gene of Interest
- 2.2. DNA Vector Construction
- 2.3. Gene Transfer to Host Systems
- 3. Manipulation of Microbial Therapeutic Enzymes for Desired Attributes
- 3.1. Site Directed Mutagenesis
- 3.2. Directed Evolution
- 3.3. Metagenomics Approach
- 4. Important Microbial Enzymes in Pharma Industry
- 4.1. L-Asparaginase
- 4.1.1. Therapeutic Application
- 4.1.1.1. Source
- 4.1.2. L-Asparaginases Properties and Activity
- 4.1.3. Enzyme Engineering Studies of L-Asparaginase
- 4.1.4. Commercial L- Asparaginase
- 4.2. Collagenase
- 4.2.1. Therapeutic Application
- 4.2.1.1. Source
- 4.2.2. Property and Activity
- 4.2.3. Engineering
- 4.2.4. Commercial Enzyme
- 4.3. Superoxide Dismutase
- 4.3.1. Therapeutic Application
- 4.3.1.1. Source
- 4.3.2. Properties and Activity
- 4.3.3. Engineering
- 4.3.4. Commercial Enzyme
- 5. Bionformatics Driven Approach in Novel Druug Discovery
- 5.1. Protein Databases
- 5.2. Structure Prediction
- 5.3. Molecular Docking
- 5.4. ADMET Properties
- Conclusion
- References
- Chapter 14
- In Silico Clinical Trials: A Broad-Spectrum Scope of CADD
- Abstract
- 1. Introduction
- 2. Computational Modeling and Algorithms in In Silico Clinical Trials
- 2.1. Phase I In Silico Clinical Trials
- 2.2. Phase II In Silico Clinical Trials
- 2.3.Phase III In Silico Clinical Trials
- 3. Tools and Softwares for In Silico Clinical Trials
- 4. Future Perspectives of In Silico Clinical Trials
- Conclusion
- Acknowledgments
- References
- About the Editors
- Index
- Blank Page
- Blank Page
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