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Applications of Molecular Dynamics Simulations in Drug Discovery
In the current drug development process, molecular dynamics (MD) simulations have proven to be very useful. This chapter provides an overview of the...
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Molecular Dynamics and Other HPC Simulations for Drug Discovery
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical...
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Automated Virtual Screening
Computational methods in modern drug discovery have become ubiquitous, with methods that cover most of the discovery stages: from hit finding and...
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Teaching Medical Students to Use Supercomputers: A Personal Reflection
At the “Kick Off” meeting for CompBioMed (compbiomed.eu), which was first funded in October 2016, I had no idea that one single sentence (“I wish I...
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Systems Biology Approach to Analyze Microarray Datasets for Identification of Disease-Causing Genes: Case Study of Oral Squamous Cell Carcinoma
The discovery of potential disease-causing genes can aid medical progress. The post-genomic era has made this a more difficult task. Modern...
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Big Data Analysis in Computational Biology and Bioinformatics
Advancements in high-throughput technologies, genomics, transcriptomics, and metabolomics play an important role in obtaining biological information...
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Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling
Living cells display dynamic and complex behaviors. To understand their response and to infer novel insights not possible with traditional...
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Effect of Muscle Forces on Femur During Level Walking Using a Virtual Population of Older Women
Aging is associated with a greater risk of muscle and bone disorders such as sarcopenia and osteoporosis. These conditions substantially affect one’s...
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Identification of Culprit Genes for Different Diseases by Analyzing Microarray Data
The identification of disease-causing genes is the first and most important step toward understanding the biological mechanisms underlying a disease....
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Optical Estimation of Bioelectric Patterns in Living Embryos
Fluorescent lifetime imaging (FLIM) is a powerful tool for visualizing physiological parameters in vivo. We present here a 3-dye strategy for map**...
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Systems Biology Modeling of Cancer Nonlinear Dynamics
Not unlike the climate or what holds the galaxies and planetary motions together, cancer biology has an intrinsic nonlinear dynamic. In this overview...
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Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins
Several databases collecting amyloidogenic regions have been released to provide information on protein sequences able to form amyloid fibrils....
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Molecular Dynamics Simulation-Based Prediction of Glycosaminoglycan Interactions with Drug Molecules
Glycosaminoglycans (GAGs) are a class of long linear anionic periodic polysaccharides. Their biological activities are very broad including tissue...
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Recent Deep Learning Applications to Structure-Based Drug Design
Identification and optimization of small molecules that bind to and modulate protein function is a crucial step in the early stages of drug...
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Efficient and Reliable Data Management for Biomedical Applications
This chapter discusses the challenges and requirements of modern Research Data Management (RDM), particularly for biomedical applications in the...
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Fluorescence Spectroscopy: A Useful Method to Explore the Interactions of Small Molecule Ligands with DNA Structures
Small molecule ligands-DNA interactions have recently received a lot of attention in the fields of life sciences, medicine, and chemical sciences. To...
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An Enhanced Quantitative Reverse Transcription-PCR Approach for Measuring Circulating MicroRNAs
Short (22 nt) RNAs called microRNAs (miRNAs) bind to and inhibit target messenger RNAs in gene regulatory networks. Recent study suggests that miRNAs...
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Metastasis Models: Thermodynamics and Complexity
The thermodynamic formalism of nonequilibrium systems together with the theory of complex systems and systems biology offer an appropriate...
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Protein–Ligand Blind Docking Using CB-Dock2
Protein–ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and...
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Emerging Trends in Big Data Analysis in Computational Biology and Bioinformatics in Health Informatics: A Case Study on Epilepsy and Seizures
Advanced technology innovations allow cost-effective, high-throughput profiling of biological systems. It enabled genome sequencing in days using...