Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: modeling and simulation approaches

A Frances-Monerris, C Hognon, T Miclot… - Journal of Proteome …, 2020 - ACS Publications
The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the
breakthrough of the COVID-19 pandemic that is presently affecting a growing number of …

How helpful were molecular dynamics simulations in sha** our understanding of SARS-CoV-2 spike protein dynamics?

JM Abduljalil, AM Elghareib, A Samir, AA Ezat… - International Journal of …, 2023 - Elsevier
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 …

UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: a comparison study

F Trozzi, X Wang, P Tao - The Journal of Physical Chemistry B, 2021 - ACS Publications
Proteins are the molecular machines of life. The multitude of possible conformations that
proteins can adopt determines their free-energy landscapes. However, the inherently high …

SARS-Cov-2 spike-S1 antigen test strip with high sensitivity endowed by high-affinity antibodies and brightly fluorescent QDs/silica nanospheres

S Tao, X Zhao, D Bao, X Liu, W Zhang… - … Applied Materials & …, 2023 - ACS Publications
The extensive research into develo** novel strategies for detecting respiratory syndrome
coronavirus 2 (SARS-CoV-2) antigens in clinical specimens, especially the sensitive point-of …

Generating tertiary protein structures via interpretable graph variational autoencoders

X Guo, Y Du, S Tadepalli, L Zhao… - Bioinformatics …, 2021 - academic.oup.com
Motivation Modeling the structural plasticity of protein molecules remains challenging. Most
research has focused on obtaining one biologically active structure. This includes the recent …

Generative adversarial learning of protein tertiary structures

T Rahman, Y Du, L Zhao, A Shehu - Molecules, 2021 - mdpi.com
Protein molecules are inherently dynamic and modulate their interactions with different
molecular partners by accessing different tertiary structures under physiological conditions …

[HTML][HTML] SARS-CoV-2—morphology, transmission and diagnosis during pandemic, review with element of meta-analysis

K Grudlewska-Buda, N Wiktorczyk-Kapischke… - Journal of Clinical …, 2021 - mdpi.com
The outbreak of Coronavirus disease 2019 (COVID-19) is caused by severe acute
respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2). Thus far, the virus has killed …

Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain

H Tian, F Trozzi, BD Zoltowski… - The Journal of Physical …, 2020 - ACS Publications
The conformational-driven allosteric protein diatom Phaeodactylum tricornutum
aureochrome 1a (PtAu1a) differs from other light–oxygen–voltage (LOV) proteins for its …

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

YS Malik, MI Ansari, JJ Kattoor, R Kaushik… - Briefings in …, 2021 - academic.oup.com
Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for
virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported …

[PDF][PDF] Generating nature-resembling tertiary protein structures with advanced generative adversarial networks (gans)

MNA Khalaf, THA Soliman… - International Journal of …, 2023 - pdfs.semanticscholar.org
In the field of molecular chemistry, the functions, interactions, and bonds between proteins
depend on their tertiary structures. Proteins naturally exhibit dynamism under different …