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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids
Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL...
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AnalysisFMO Toolkit: A PyMOL Plugin for 3D-Visualization of Interaction Energies in Proteins (3D-VIEP) Calculated by the FMO Method
Interresidue and ligand/substrate-residue interactions in a biomacromolecular system such as drug target protein variously correlated with structure,...
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Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical...
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VSFlow: an open-source ligand-based virtual screening tool
Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to...
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Molecular Docking Studies on the Binding Affinity of Alpha-Conotoxins on Voltage-Gated Sodium Ion Channel Using an Incremental Genetic Algorithm Approach
The α-conotoxins are neurotoxic peptides produced during predation and defense mechanisms of Conus organisms. Previous studies focused on their...
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Studies of the symmetric binding mode of daclatasvir and analogs using a new homology model of HCV NS5A GT-4a
ContextEgypt has a high prevalence of the hepatitis C virus (HCV) genotype 4a (GT-4a). Unfortunately, the high resistance it exhibited still was not...
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Computational screening of phytocompound isolated from the plant Toddalia asiatica and Coleonema album as potential inhibitors against enzyme DPP-4 as a treatment for Type-2 Diabetes mellitus
Human hormone glucagon-like peptide-1 (GLP-1) lowers α-cell glucagon and increases β -cell insulin. GLP-1 is digested by dipeptidyl peptidase (DPP-4)...
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Mechanism of Erzhiwan in treating osteoporosis based on molecular docking technology and molecular dynamics simulation
This experiment was a network pharmacology research based on the theoretical system of traditional Chinese medicine. TCMSP database, PubChem...
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Structural requirement of RARγ agonism through computational aspects
ContextRARγ is a therapeutic target for many skin diseases and has potential in cancer treatment. In the current study, we put forward a...
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Molecular dynamic simulation suggests stronger interaction of Omicron-spike with ACE2 than wild but weaker than Delta SARS-CoV-2 can be blocked by engineered S1-RBD fraction
The SARS-CoV-2 claimed millions of lives, globally. Occurring from Wuhan (wild type) in December, 2019, it constantly mutated to Omicron (B.1.1.529),...
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Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy
Assessment of target druggability guided by search and characterization of hot spots is a pivotal step in early stages of drug-discovery. The raw...
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RNA 3D Structure Comparison Using RNA-Puzzles Toolkit
Computational modeling of RNA three-dimensional (3D) structure may help in unrevealing the molecular mechanisms of RNA molecules and in designing...
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Molecular Cloning, Expression and Enzymatic Characterization of Tetrahymena thermophila Glutathione-S-Transferase Mu 34
Glutathione-S-transferase enzymes (GSTs) are essential components of the phase II detoxification system and protect organisms from oxidative stress...
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In silico-guided discovery and in vitro validation of novel sugar-tethered lysinated carbon nanotubes for targeted drug delivery of doxorubicin
ContextMultiwalled carbon nanotubes (MWCNTs) functionalized with lysine via 1,3-dipolar cycloaddition and conjugated to galactose or mannose are...
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RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology
The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a...
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Engineered Protease-Responsive RNA-Binding Proteins (RBPs) to Expand the Toolbox of Synthetic Circuits in Mammalian Cells
Genetically encoded sensor–actuator circuits aim at reprogramming cellular functions and are inspired by intracellular networks: from the input...
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Nano-Informatics: Studies on Nano Information Platforms and Their Application in Various Sectors
Nano-informatics is the interdisciplinary area that investigates the application of information technology on nanobiotechnological data. It is...
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Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry
Hydrogen/deuterium exchange (HDX) followed by mass spectrometry detection (MS) provides a fast, reliable, and detailed solution for the assessment of...
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Unraveling the Mechanisms of Cannabidiol’s Pharmacological Actions: A Comprehensive Research Overview
Cannabis sativa has long been used for neurological and psychological healing. Recently, cannabidiol (CBD) extracted from cannabis sativa has gained...
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Interaction of Tau with G-Protein-Coupled Purinergic P2Y12 Receptor by Molecular Docking and Molecular Dynamic Simulation
Alzheimer’s disease, a progressive neurological disorder, is characterized by the accumulation of neurofibrillary tangles and senile plaques by Tau...