[HTML][HTML] A guide to in silico drug design
Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …
few candidates progress from hit compound to a commercially available product, often due …
Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein
V Calvaresi, AG Wrobel, J Toporowska… - Nature …, 2023 - nature.com
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane
fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 …
fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 …
[HTML][HTML] Variations within the glycan shield of SARS-CoV-2 impact viral spike dynamics
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether
arisen naturally or through vaccination. Understanding the structure of the viral spike assists …
arisen naturally or through vaccination. Understanding the structure of the viral spike assists …
Mechanisms of allostery at the viral surface through the eyes of molecular simulation
The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such
layers have traditionally been thought of as immovable structures, but it is becoming …
layers have traditionally been thought of as immovable structures, but it is becoming …
Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2 via allosteric disulfide disruption in the spike glycoprotein
The development of small-molecules targeting different components of SARS-CoV-2 is a key
strategy to complement antibody-based treatments and vaccination campaigns in managing …
strategy to complement antibody-based treatments and vaccination campaigns in managing …
SARS-CoV2 billion-compound docking
This dataset contains ligand conformations and docking scores for 1.4 billion molecules
docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro …
docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro …
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike …
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth
advantage and increased viral fitness by acquiring convergent mutations, suggesting that …
advantage and increased viral fitness by acquiring convergent mutations, suggesting that …
Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA. 1 and BA. 2 Trimers: Mutation …
G Verkhivker, M Alshahrani, G Gupta - Viruses, 2023 - mdpi.com
A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA. 1 and
BA. 2 variants revealed a considerable plasticity of the spike protein and the emergence of …
BA. 2 variants revealed a considerable plasticity of the spike protein and the emergence of …
SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade
Accumulating evidence indicates a potential role for bacterial lipopolysaccharide (LPS) in
the overactivation of the immune response during SARS-CoV-2 infection. LPS is recognized …
the overactivation of the immune response during SARS-CoV-2 infection. LPS is recognized …
Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA. 2, BA. 2.75 and XBB. 1 Spike …
In the current study, we explore coarse-grained simulations and atomistic molecular
dynamics together with binding energetics scanning and cryptic pocket detection in a …
dynamics together with binding energetics scanning and cryptic pocket detection in a …