Link roundup: Apr–Dec 2022
Published:
Science
Wood spirits: How Japan made the world’s first liquor from trees
The price of ‘sugar free’: are sweeteners as harmless as we thought?
A language model beats alphafold2 on orphans
https://github.com/FellowsFreiesWissen/computational_notebooks Why Conventional Wisdom About Cancer Can Be Misleading
Machine Learning to Handle the Proteome
‘The entire protein universe’: AI predicts shape of nearly every known protein
Could machine learning fuel a reproducibility crisis in science?
Blots on a field?
PNAS | Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes
Breaking into the black box of artificial intelligence
Others
When a Houseplant Obsession Becomes a Nightmare
Book Review: What We Owe The Future
If Someone Is Typing, Then Stops … Can I Ask Why?
One can envisage several alternatives to further enhance VS predictions if experiments are not accessible/available. More than one score function might be combined to produce a consensus top-ranked list, while X-ray screening have recently identified allosteric sites that might provide a wider description of virus target. In addition, pockets are not static but prone to modifications in in vivo conditions, and a preliminary molecular dynamics (MD) stage could be implemented to produce trajectories of the targets.33 A series of representative structures (or clusters) can be subsequently used for conducting VS simulations. MD might be also used to confirm the stability of the binding pose.Finally, the simulation of a reduced number of drugs allows to use of more advanced levels of theory, e. g., ab initio or multiscale QM/MM.
– When Virtual Screening Yields Inactive Drugs: Dealing with False Theoretical Friends
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