Computational Modelling and Simulation in Biomedical Research
1st Edition
Published on 15. August 2024
160 pages
978-981-5165-46-3 (ISBN)
Description
No detailed description available for "Computational Modelling and Simulation in Biomedical Research".
More details
Other editions
Additional editions
Yee Siew Choong
Computational Modeling and Simulation in Biomedical Research
Book
08/2024
Bentham Science Publishers
€61.77
Shipment within 3-4 weeks
Content
- Cover
- Title
- Copyright
- End User License Agreement
- Contents
- Preface
- List of Contributors
- Dedication
- Introduction to Computational Tools in Biomedical Research
- Chong Lee Ng1 and Yee Siew Choong1,*
- INTRODUCTION
- ROLES OF COMPUTATIONAL TOOLS IN SEQUENCE ALIGNMENT AND STRUCTURAL STUDIES
- General Applications of Computational Tools in Sequence and Structural Studies
- Studying the Interactions between Antibody against MDM2 Antigen
- Repurposing Existing Approved Drugs against SARS-CoV2 Proteins
- ROLES OF COMPUTATIONAL TOOLS IN UNDERSTANDING PROTEIN DYNAMICS
- General Applications of Computational Molecular Dynamic Simulation
- Computational Optimization of Antibody Affinity toward Heat Shock Protein (HSP16.3) Antigen
- Elucidating the Catalytic Reaction of Isocitrate Lyase in Mycobacterium tuberculosis
- ROLES OF COMPUTATIONAL TOOLS IN CELLULAR ACTIVITY AND SYSTEM BIOLOGY
- Application of Computational Tools in Predictions of Cellular Activity and System Biology
- Changes in p53 Protein Expression Affects the Cellular Apoptosis
- Computational Pharmacokinetic Prediction of Anticancer Phytocompounds
- CONCLUDING REMARKS
- ACKNOWLEDGEMENT
- REFERENCES
- Computational Analysis of Biological Data: Where Are We?
- Lilach Soreq1 and Wael Mohamed2,3,*
- INTRODUCTION
- GENOMIC DATA ANALYSIS
- Genetic Analyses of Expression Data
- Circular RNAs
- RNA Interference
- BDNF
- Public Database for Genomics Data
- BIG DATA IN LIFE SCIENCE
- Use of Disease Mice Model as a Comparative Model
- DIRECT ADMINISTRATION OF SIRNA FOR THERAPEUTICS
- Huntington's Disease (HD)
- Amyotrophic Lateral Sclerosis (ALS) Disease
- CRISPR Gene Therapy
- Human iPSC-Derived Sensory Neurons
- NOVEL CLASSES OF NON-CODING RNAS
- DEEP BRAIN STIMULATION (DBS) AND PARKINSON'S DISEASE (PD)
- APPLICATIONS OF RNA INTERFERENCE-BASED THERAPEUTICS
- Antisense-Based Therapeutics
- Multiple Sclerosis
- Post-traumatic Stress Disorder (PTSD)
- CONCLUSION AND PERSPECTIVES
- FUNDING
- REFERENCES
- Algorithm Development for Computational Modeling and Simulation
- Nordina Syamira Mahamad Shabudin1 and Ahmad Naqib Shuid1,*
- INTRODUCTION
- Computational Tertiary Structure Prediction Protocol
- Free Modelling Approach for Tertiary Protein Structure Prediction
- Bhageerath-H
- RaptorX-Contact
- Template-Based Tertiary Protein Structure Modelling
- Threading
- NDThreader
- Homology Modeling
- IntFOLD6-TS
- Protein Structure Refinement
- Molecular Dynamic Simulation for Protein Refinement
- Refinement programs Link/Address
- Molecular Dynamic Approaches for Protein Refinement
- Quality Assessment of Predicted Tertiary Protein Structure
- The Single-Model Based Quality Assessment Approach - ProQ2
- The Cluster-Based Quality Assessment Approach
- The Quasi-single Model Quality Assessment Approach
- The Artificial Neural Network (ANN) and Deep Learning-Based Model Quality Assessment - ModFOLD8
- Deoxyribonucleic Acid Sequencing
- The Cluster-Based Quality Assessment Approach
- Hashed-Based Genome Mapping
- The Suffix-Tree Approach
- Burrow-Wheeler Transform Approach
- The Fast Fourier Transform Approach
- The Approximate Matching Approach
- The Smith-Waterman and Needleman-Wunsch Approach
- The Coevolutionary Neural Network (CNN) Approach
- The Mechanism of Docking Protocol
- The Search Algorithm
- The Rigid Body Docking and Flexible-ligand Docking Body
- The Systematic Search Algorithm
- The Exhaustive Search Algorithm
- The Fragment-Based Algorithm
- The Incremental Algorithm
- The Distance Geometry
- The Fast Shape Matching
- The Stochastic or Random Search Methods
- Monte-Carlo Simulation
- The Genetic Algorithm
- The Tabu Search Algorithm
- The Molecular Dynamic Simulation Approaches
- The Scoring Function
- The Force Field-Based Scoring
- The Empirical Scoring
- The Knowledge-based scoring
- The Consensus-Based Scoring
- CONCLUSION
- FUNDING
- REFERENCES
- The Roles and Application of Protein Modeling in Biomedical Research
- Chong Lee Ng1, Tze Yin Lee1, Nur Naili Irsyada Binti Zulkfli1, Theam Soon Lim1 and Yee Siew Choong1,*
- INTRODUCTION
- THE EFFECTS OF PROTEIN MUTATION
- PROTEIN STRUCTURE DETERMINATION BY EXPERIMENTAL METHODS
- Protein Sequencing
- X-ray Crystallography
- Nuclear Magnetic Resonance (NMR) Spectroscopy
- Cryogenic-Electron Microscopy (Cryo-EM)
- Advantages and Limitations in Protein Structure Determination by Experimental Methods
- The advantages and Limitations of X-ray Crystallography
- The advantages and limitations of NMR spectroscopy
- The advantages and limitations of cryo-EM
- COMPUTATIONAL METHODS IN PROTEIN STRUCTURE PREDICTION
- Ab Initio Method
- Comparative Modeling
- Threading Method
- Limitations in Protein Structure Determination by Computational Methods
- APPLICATIONS OF PROTEIN MODELING IN BIOMEDICAL RESEARCH
- Screening of Phytochemicals as Anti-Viral Agents against NSP1 Protein in SARS-CoV-2
- Investigating the Interactions between DNA-Binding Motif of Transcription Factors and DNA
- Optimization of the Binding Affinity of Antibody toward Heat Shock Protein
- Studying the Interactions between S-Protein Variants from SARS-CoV-2 and Human Angiotensin-Converting Enzyme (hACE2)
- CONCLUDING REMARKS
- ACKNOWLEDGEMENT
- REFERENCES
- Dynamics of Biomolecular Ligand Recognition
- Ilija Cvijetic1, Dusan Petrovic2 and Mire Zloh3,4,*
- INTRODUCTION
- PHARMACOPHORE MODELING
- Dynamic Pharmacophores
- MOLECULAR DOCKING
- MOLECULAR DYNAMICS WITH ENHANCED SAMPLING
- PERSPECTIVES
- CONCLUSION
- ACKNOWLEDGEMENT
- REFERENCES
- Subject Index
