Computational Modelling and Simulation in Biomedical Research

Table of Contents

• LIST OF CONTRIBUTORS
• DEDICATION

• RESEARCH
• Chong Lee Ng and Yee Siew Choong
• 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

• Lilach Soreq and Wael Mohamed
• 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

• SIMULATION
• Nordina Syamira Mahamad Shabudin and Ahmad Naqib Shuid
• 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

• BIOMEDICAL RESEARCH
• Chong Lee Ng, Tze Yin Lee, Nur Naili Irsyada Binti Zulkfli, Theam Soon Lim and Yee
• Siew Choong
• 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

• Ilija Cvijetić, Dušan Petrović and Mire Zloh
• INTRODUCTION
• PHARMACOPHORE MODELING
• Dynamic Pharmacophores
• MOLECULAR DOCKING
• MOLECULAR DYNAMICS WITH ENHANCED SAMPLING
• PERSPECTIVES
• CONCLUSION
• ACKNOWLEDGEMENT
• REFERENCES
• SUBJECT INDEX