Collective variable-based enhanced sampling and machine learning
M Chen - The European Physical Journal B, 2021 - Springer
Collective variable-based enhanced sampling methods have been widely used to study
thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced …
thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced …
[HTML][HTML] Allosteric binding sites of the SARS-CoV-2 main protease: potential targets for broad-spectrum anti-coronavirus agents
The current pandemic caused by the COVID-19 disease has reached everywhere in the
world and has affected every aspect of our lives. As of the current data, the World Health …
world and has affected every aspect of our lives. As of the current data, the World Health …
Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
Parallel cascade selection molecular dynamics-based ligand binding-path sampling (LB-
PaCS-MD) was combined with fragment molecular orbital (FMO) calculations to reveal the …
PaCS-MD) was combined with fragment molecular orbital (FMO) calculations to reveal the …
High-dimensional fluctuations in liquid water: Combining chemical intuition with unsupervised learning
The microscopic description of the local structure of water remains an open challenge. Here,
we adopt an agnostic approach to understanding water's hydrogen bond network using data …
we adopt an agnostic approach to understanding water's hydrogen bond network using data …
The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro
Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) the
WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to …
WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to …
DADApy: Distance-based analysis of data-manifolds in Python
DADApy is a Python software package for analyzing and characterizing high-dimensional
data manifolds. It provides methods for estimating the intrinsic dimension and the probability …
data manifolds. It provides methods for estimating the intrinsic dimension and the probability …
Key allosteric and active site residues of SARS-CoV-2 3CLpro are promising drug targets
The main protease of SARS-CoV-2, 3-chymotrypsin-like protease (3CLpro), is a prominent
target for antiviral development due to its essential role in the viral life cycle. Research has …
target for antiviral development due to its essential role in the viral life cycle. Research has …
Tuning proton transfer thermodynamics in SARS-CoV-2 main protease: implications for catalysis and inhibitor design
The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT)
from Cys145 to His41. The same PT is likely also required for the covalent binding of some …
from Cys145 to His41. The same PT is likely also required for the covalent binding of some …
Beyond local structures in critical supercooled water through unsupervised learning
The presence of a second critical point in water has been a topic of intense investigation for
the last few decades. The molecular origins underlying this phenomenon are typically …
the last few decades. The molecular origins underlying this phenomenon are typically …
Interfacial water many-body effects drive structural dynamics and allosteric interactions in SARS-CoV-2 main protease dimerization interface
Following our previous work (Chem. Sci. 2021, 12, 4889− 4907), we study the structural
dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of …
dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of …