Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating
topological entities can be either useful or cumbersome. In recent decades, the importance …

The specific activity of enzymes can be altered over long timescales in cells by synonymous
mutations that alter a messenger RNA molecule's sequence but not the encoded protein's …

The fact that proteins can have their chain formed in a knot is known for almost 30 years.
However, as they are not common, only a fraction of such proteins is available in the Protein …

The last decade has shown that there are an increasing numbers of known proteins that
contain linear open knots or slipknots in their native folded structure. In general, knots in …

The computer artificial intelligence system AlphaFold has recently predicted previously
unknown three‐dimensional structures of thousands of proteins. Focusing on the subset with …

Twenty years after their discovery, knots in proteins are now quite well understood. They are
believed to be functionally advantageous and provide extra stability to protein chains. In this …

Coarse-grained, self-contained polymer models are powerful tools in the study of protein
folding. They are also essential to assess predictions from less rigorous theoretical …

Molecular dynamics simulations have emerged as a powerful tool to study biological
systems at varied length and timescales. The conventional all-atom molecular dynamics …

Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as
significant structural motifs. Seven distinctly knotted folds have already been identified. It is …