New Insights into the Cooperativity and Dynamics of Dimeric Enzymes
KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …
forms, with about half of those found in the UniProt database being homodimeric …
Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery
Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …
drug molecules. A critical factor in this process is the binding affinity between candidate …
Uncertainty quantification in classical molecular dynamics
Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …
systems on the atomistic scale. It finds applications from physics and chemistry to …
[HTML][HTML] Structural requirements and interaction mechanisms of ACE inhibitory peptides: Molecular simulation and thermodynamics studies on LAPYK and its modified …
B Zhang, J Liu, H Wen, F Jiang, E Wang… - Food Science and Human …, 2022 - Elsevier
The understanding of the structural requirements and the intermolecular-interaction
mechanism are important for discovering potent angiotensin-converting enzyme (ACE) …
mechanism are important for discovering potent angiotensin-converting enzyme (ACE) …
Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions
Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …
applications in drug optimization. A series of congeneric compounds are generated from a …
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations
Active learning (AL) is a specific instance of sequential experimental design and uses
machine learning to intelligently choose the next data point or batch of molecular structures …
machine learning to intelligently choose the next data point or batch of molecular structures …
Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …
role in the drug discovery process as well as in personalized medicine. Of considerable …
Ensembles are required to handle aleatoric and parametric uncertainty in molecular dynamics simulation
Classical molecular dynamics is a computer simulation technique that is in widespread use
across many areas of science, from physics and chemistry to materials, biology, and …
across many areas of science, from physics and chemistry to materials, biology, and …
On the calculation of equilibrium thermodynamic properties from molecular dynamics
The purpose of statistical mechanics is to provide a route to the calculation of macroscopic
properties of matter from their constituent microscopic components. It is well known that the …
properties of matter from their constituent microscopic components. It is well known that the …
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations
DNA can be folded into rationally designed, unique, and functional materials. To fully realise
the potential of these DNA materials, a fundamental understanding of their structure and …
the potential of these DNA materials, a fundamental understanding of their structure and …