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Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method
Water molecules play a crucial role in protein–ligand binding, and many tools exist that aim to predict the position and relative energies of these...
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Interactions between the protein barnase and co-solutes studied by NMR
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some...
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Enhancement of catalytic activity and alkaline stability of cellobiohydrolase by structure-based protein engineering
Alkaline cellobiohydrolases have the potential for application in various industries, including pulp processing and laundry where operation under...
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Computational identification of bioactive compounds from Cydonia oblonga Mill. against hepatocellular carcinoma by targeting pTEN and HBx-interacting protein
Phytochemicals derived from Cydonia oblonga have been investigated for their anti-oxidant and anti-cancer activities in various cancer cell lines....
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Battling BTK mutants with noncovalent inhibitors that overcome Cys481 and Thr474 mutations in Waldenström macroglobulinemia therapy: structural mechanistic insights on the role of fenebrutinib
Recently, the non-covalent Bruton tyrosine kinase (BTK) inhibitor fenebrutinib was presented as a therapeutic option with strong inhibitory efficacy...
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Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants
ObjectiveThe COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe...
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How can the cisplatin analogs with different amine act on DNA during cancer treatment theoretically?
Cisplatin is a widely used anti-cancer drug which inhibits the replication and polymerization of DNA molecule while showing some side effects and...
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Biodegradation of anionic polyacrylamide by manganese peroxidase: docking, virtual mutation based on affinity, QM/MM calculation and molecular dynamics simulation
Manganese peroxidase (Mn P) is capable of effectively degrading anionic polyacrylamide (HPAM). However, the interaction of Mn P with HPAM at...
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First-principle study on the electronic transport properties of 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (a diarylethene) as an optical molecular switch
In this research, the electronic transport of 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (as a diarylethene) and 2 of its...
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Electric and Magnetic Evaluation of Aluminum–Magnesium Nanoalloy Decorated with Germanium Through Heterocyclic Carbenes Adsorption: A Density Functional Theory Study
AbstractHeterocyclic compounds with multiple bonds and heteroatoms of nitrogen, oxygen and sulfur can be notable as corrosion inhibitors for metal...
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Analysis of cholesterol-recognition motifs of the plasma membrane Ca2+-ATPase
The plasma membrane Ca 2+ -ATPase (PMCA) is crucial for the fine tuning of intracellular calcium levels in eukaryotic cells. In this study, we show the...
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Stretching Elasticity and Flexibility of Single Polyformaldehyde Chain
In this work, the single-chain elasticity of polyformaldehyde (POM) is studied, for the first time, by employing atomic force microscopy (AFM)-based...
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Current Understanding on the Unique Relaxation Dynamics of Sub-nanometer Materials and Their Structure-Property Relationships
Sub-nanometer materials(SNMs) define the emergent functional material system with their characteristic dimensions at sub-1 nm scale and they can be...
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Quantum chemical evaluation, QSAR analysis, molecular docking and dynamics investigation of s-triazine derivatives as potential anticancer agents
Recent studies have shown that 1,3,5-triazine (s-triazine) derivatives are potent anticancer agents. The optimized geometry and vibrational...
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Impact of Drug Repurposing on SARS-Cov-2 Main Protease
AbstractThe recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public...
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A 3-position modified naphthalimide fluorescent probe for reversible response to H2O2 and GSH and cell imaging
An “off–on–off” fluorescent probe NapEb for high selectivity and reversible response to H 2 O 2 and GSH was synthesized. Inspired by the role of GSH in...
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Probing the inhibition of MAO-B by chalcones: an integrated approach combining molecular docking, ADME analysis, MD simulation, and MM-PBSA calculations
ContextMonoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable...
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The Electron Density
In this chapter we analyze the basic scalar field in the topological theories of the chemical bond, the electron density,...
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Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis
Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of...
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A DFT Study on the Direct CF2 Fragmentation Mechanisms of 1,3-C4F6 and 1,3-C4F6+ in Plasma
Elucidation of the CF 2 generation mechanism in 1,3-C 4 F 6 gas plasma has been one of the important issues for experimental and theoretical researchers...
