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Virtual Screening Process: A Guide in Modern Drug Designing
Due to its capacity to drastically cut the cost and time necessary for experimental screening of compounds, virtual screening (VS) has grown to be a...
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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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New Insights into Clinical Management for Sickle Cell Disease: Uncovering the Significant Pathways Affected by the Involvement of Sickle Cell Disease
One of the severe monogenic conditions with the highest prevalence in the globe is sickle cell disease. Although the significance of chronic anemia,...
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Big Data in Bioinformatics and Computational Biology: Basic Insights
The human genome was first sequenced in 1994. It took 10 years of cooperation between numerous international research organizations to reveal a...
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Computer-Aided Drug Discovery and Design: Recent Advances and Future Prospects
Computer-aided drug discovery and design involve the use of information technologies to identify and develop, on a rational ground, chemical...
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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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Hubs and Bottlenecks in Protein-Protein Interaction Networks
Protein-protein interaction networks (PPINs) represent the physical interactions among proteins in a cell. These interactions are critical in all...
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Inference of Dynamic Growth Regulatory Network in Cancer Using High-Throughput Transcriptomic Data
Growth is regulated by gene expression variation at different developmental stages of biological processes such as cell differentiation, disease...
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Systems Biology Approaches to Understanding COVID-19 Spread in the Population
In essence, the COVID-19 pandemic can be regarded as a systems biology problem, with the entire world as the system, and the human population as the...
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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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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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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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Accelerating the Discovery and Design of Antimicrobial Peptides with Artificial Intelligence
Peptides modulate many processes of human physiology targeting ion channels, protein receptors, or enzymes. They represent valuable starting points...
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Cellular Blood Flow Modeling with HemoCell
Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and...
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Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities
Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages....
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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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HPC Framework for Performing in Silico Trials Using a 3D Virtual Human Cardiac Population as Means to Assess Drug-Induced Arrhythmic Risk
Following the 3 R’s principles of animal research—replacement, reduction, and refinement—a high-performance computational framework was produced to...
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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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High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques
Structure-based drug design (SBDD) is rapidly evolving to be a fundamental tool for faster and more cost-effective methods of lead drug discovery....
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A Blood Flow Modeling Framework for Stroke Treatments
Circulatory models can significantly help develop new ways to alleviate the burden of stroke on society. However, it is not always easy to know what...