Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …

Around 6% of protein structures deposited in the PDB are entangled, forming knots,
slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves …

The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

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 protein topology database KnotProt, http://knotprot. cent. uw. edu. pl/, collects
information about protein structures with open polypeptide chains forming knots or slipknots …

Highlights•Knotted proteins span diverse biological functions and cover∼ 1% of all PDB
entries.•Reaching their knotted native states requires a concerted series of folding …

Computational simulations of protein folding can be used to interpret experimental folding
results, to design new folding experiments, and to test the effects of mutations and small …

Knotted proteins have their native structures arranged in the form of an open knot. In the last
ten years researchers have been making significant efforts to reveal their folding mechanism …

AlphaFold is a groundbreaking deep learning tool for protein structure prediction. It achieved
remarkable accuracy in modeling many 3D structures while taking as the user input only the …

Knots in proteins are increasingly being recognized as an important structural concept, and
the folding of these peculiar structures still poses considerable challenges. From a functional …