Computational Modelling and Simulation in Biomedical Research

Name: Computational Modelling and Simulation in Biomedical Research | Towards Communication in CAAD. Spectral Characterisation and Modelling with Conjugate Symbolic Domains
Brand: De Gruyter
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Towards Communication in CAAD. Spectral Characterisation and Modelling with Conjugate Symbolic Domains

Yee Siew Choong(Autor*in)

De Gruyter (Verlag)

1. Auflage

Erschienen am 15. August 2024

160 Seiten

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978-981-5165-46-3 (ISBN)

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Inhalt

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

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