How helpful were molecular dynamics simulations in sha** our understanding of SARS-CoV-2 spike protein dynamics?
The SARS-CoV-2 spike protein (S) represents an important viral component that is required
for successful viral infection in humans owing to its essential role in recognition of and entry …
for successful viral infection in humans owing to its essential role in recognition of and entry …
Many roles of carbohydrates: A computational spotlight on the coronavirus S protein binding
Glycosylation is one of the post-translational modifications with more than 50% of human
proteins being glycosylated. The exact nature and chemical composition of glycans are …
proteins being glycosylated. The exact nature and chemical composition of glycans are …
A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for
understanding the mechanisms by which they recognize one another and reversibly …
understanding the mechanisms by which they recognize one another and reversibly …
Boosting Enzyme Activity in Biomass Conversion by Modulating the Hydrolysis Process of Cellobiohydrolases
H Liu, Y Ding, S Mazurkewich, W Pei, X Wei… - ACS …, 2024 - ACS Publications
Cellobiohydrolases (CBHs) are the most significant cellulose-degrading enzymes, the
performance of which determines the cost-effective utilization of renewable lignocellulosic …
performance of which determines the cost-effective utilization of renewable lignocellulosic …
A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo
B Havranek, GW Lindsey, Y Higuchi, Y Itoh… - Communications …, 2023 - nature.com
Abstract SARS-CoV-2, especially B. 1.1. 529/omicron and its sublineages, continues to
mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity …
mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity …
Achieving Accurate Standard Protein–Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling
A new strategy for the prediction of binding free energies of protein–protein complexes is
reported in the present article. By combining an ergodic-sampling algorithm with the so …
reported in the present article. By combining an ergodic-sampling algorithm with the so …
Binding affinity estimation from restrained umbrella sampling simulations
The protein–ligand binding affinity quantifies the binding strength between a protein and its
ligand. Computer modeling and simulations can be used to estimate the binding affinity or …
ligand. Computer modeling and simulations can be used to estimate the binding affinity or …
How SARS-CoV-2 alters the regulation of gene expression in infected cells
Nonstructural accessory proteins in viruses play a key role in hijacking the basic cellular
mechanisms, which is essential to promote the virus survival and evasion of the immune …
mechanisms, which is essential to promote the virus survival and evasion of the immune …
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease …
Absolute binding free energy (ABFE) calculations can be an important part of the drug
discovery process by identifying molecules that have the potential to be strong binders for a …
discovery process by identifying molecules that have the potential to be strong binders for a …
SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study
The emergence of the variant of concern Omicron (B. 1.1. 529) of severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high …
syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high …