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Homology Modeling Methods and Protocols
This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology...
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Homology Modeling of Transporter Proteins
Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological...
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Protein Homology Modeling for Effective Drug Design
The effective drug design, especially for combating the multi-drug-resistant bacterial pathogens, requires more and more sophisticated procedures to...
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Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling
Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the Protein...
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Homology Modeling of the G Protein-Coupled Receptors
G protein-coupled receptors (GPCRs) are therapeutically important family of membrane proteins. Despite growing number of experimental structures...
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Contact-Assisted Threading in Low-Homology Protein Modeling
The ability to successfully predict the three-dimensional structure of a protein from its amino acid sequence has made considerable progress in the...
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Homology Modeling of Antibody Variable Regions: Methods and Applications
Adaptive immunity specifically protects us from antigenic challenges. Antibodies are key effector proteins of adaptive immunity, and they are...
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Specificities of Protein Homology Modeling for Allosteric Drug Design
The allosteric binding sites are usually located in the flexible areas of proteins, which are hardly visible in the crystal structures. However,...
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Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis
The analysis of the relationship between sequence and structure similarities during the evolution of a protein family has revealed a limit of...
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In silico homology modeling of dengue virus non-structural 4B (NS4B) protein and its molecular docking studies using triterpenoids
BackgroundDengue fever has become a significant worldwide health concern, because of its high morbidity rate and the potential for an increase in...
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Homotopy, homology, and persistent homology using closure spaces
We develop persistent homology in the setting of filtrations of (Čech) closure spaces. Examples of filtrations of closure spaces include metric...
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Homology modeling of Forkhead box protein C2: identification of potential inhibitors using ligand and structure-based virtual screening
Overexpression of Forkhead box protein C2 (FOXC2) has been associated with different types of carcinomas. FOXC2 plays an important role in the...
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Homology Modeling, Screening, and Identification of Potential FOXO6 Inhibitors Curtail Gastric Cancer Progression: an In Silico Drug Repurposing Approach
Gastric cancer is the world’s second leading cause of cancer-related fatalities, with the epidemiology changing over the previous several decades....
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Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle
NrfA is the molecular marker for dissimilatory nitrate reduction to ammonium (DNRA) activity, catalysing cytochrome c nitrite reductase enzyme....
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Persistent Homology for RNA Data Analysis
Molecular representations are of great importance for machine learning models in RNA data analysis. Essentially, efficient molecular descriptors or...
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Quantifying the Structural Stability of Simplicial Homology
Simplicial complexes are generalizations of classical graphs. Their homology groups are widely used to characterize the structure and the topology of...
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Virtual screening of PEBP1 inhibitors by combining 2D/3D-QSAR analysis, hologram QSAR, homology modeling, molecular docking analysis, and molecular dynamic simulations
Human phosphatidylethanolamine binding protein 1 (hPEBP1) is a novel target affecting many cellular signaling pathways involved in the formation of...
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Abandoned Object Detection Using Persistent Homology
The automatic detection of suspicious abandoned objects has become a priority in video surveillance in the last years. Terrorist attacks, improperly...
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QSAR, homology modeling, and docking simulation on SARS-CoV-2 and pseudomonas aeruginosa inhibitors, ADMET, and molecular dynamic simulations to find a possible oral lead candidate
BackgroundIn seek of potent and non-toxic iminoguanidine derivatives formerly assessed as active Pseudomonas aeruginosa inhibitors, a combined...
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DFT and Persistent Homology for Topological Musical Data Analysis
There are several works that already exist in the context of persistent homology for Topological Musical Data Analysis, and we can cite [2] and [3]...