Uncertainty quantification in classical molecular dynamics
S Wan, RC Sinclair… - … Transactions of the …, 2021 - royalsocietypublishing.org
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 …
Artificial intelligence in drug design: algorithms, applications, challenges and ethics
AA Arabi - Future Drug Discovery, 2021 - Taylor & Francis
The discovery paradigm of drugs is rapidly growing due to advances in machine learning
(ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug …
(ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug …
Prediction of binding free energy of protein–ligand complexes with a hybrid molecular mechanics/generalized born surface area and machine learning method
L Dong, X Qu, Y Zhao, B Wang - ACS omega, 2021 - ACS Publications
Accurate prediction of protein–ligand binding free energies is important in enzyme
engineering and drug discovery. The molecular mechanics/generalized Born surface area …
engineering and drug discovery. The molecular mechanics/generalized Born surface area …
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning-and physics-based simulations on high …
The race to meet the challenges of the global pandemic has served as a reminder that the
existing drug discovery process is expensive, inefficient and slow. There is a major …
existing drug discovery process is expensive, inefficient and slow. There is a major …
Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
The accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a
considerable challenge in computer-aided drug discovery. Recently, it has been …
considerable challenge in computer-aided drug discovery. Recently, it has been …
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics
P Procacci - Current Opinion in Structural Biology, 2021 - Elsevier
Highlights•Computational approaches are becoming an essential tool in modern drug
design.•Development of automated workflows from docking to MD techniques for drug …
design.•Development of automated workflows from docking to MD techniques for drug …
Scalable HPC & AI infrastructure for COVID-19 therapeutics
COVID-19 has claimed more than 2.7× 106 lives and resulted in over 124× 106 infections.
There is an urgent need to identify drugs that can inhibit SARS-CoV-2. We discuss …
There is an urgent need to identify drugs that can inhibit SARS-CoV-2. We discuss …
TIES 20: Relative binding free energy with a flexible superimposition algorithm and partial ring morphing
The TIES (Thermodynamic Integration with Enhanced Sampling) protocol is a formally exact
alchemical approach in computational chemistry to the calculation of relative binding free …
alchemical approach in computational chemistry to the calculation of relative binding free …
The effect of protein mutations on drug binding suggests ensuing personalised drug selection
The advent of personalised medicine promises a deeper understanding of mechanisms and
therefore therapies. However, the connection between genomic sequences and clinical …
therefore therapies. However, the connection between genomic sequences and clinical …
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge
Free energy drives a wide range of molecular processes such as solvation, binding,
chemical reactions and conformational change. Given the central importance of binding, a …
chemical reactions and conformational change. Given the central importance of binding, a …