Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak,
there has been an increasing interest in finding a potential therapeutic agent for the disease …

Highlights•Biochemical data can be represented with text-based languages codified by
humans.•Natural language processing (NLP) can be applied to textual biochemical …

Reports of successful applications of machine learning (ML) methods in structure-based
virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks …

One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …

Most chemical experiments are planned by human scientists and therefore are subject to a
variety of human cognitive biases, heuristics and social influences. These anthropogenic …

Motivation: Most bioactive molecules perform their action by interacting with proteins or other
macromolecules. However, for a significant fraction of them, the primary target remains …

Results of a previous docking study are reanalyzed and extended to include results from the
docking program FRED and a detailed statistical analysis of both structure reproduction and …

Undetected overfitting can occur when there are significant redundancies between training
and validation data. We describe AVE, a new measure of training–validation redundancy for …

Benchmarks for molecular docking have historically focused on re-docking the cognate
ligand of a well-determined protein–ligand complex to measure geometric pose prediction …

In his philosophic musings “Meditations” the Emperor Marcus Aurelius asks “This thing, what
is it in itself, in its own constitution? What is its substance and material? And what its causal …