New 63 knot and other knots in human proteome from AlphaFold predictions

AlphaFold is a new, highly accurate machine learning protein structure prediction method that outperforms other methods. Recently this method was used to predict the structure of 98.5% of human proteins. We analyze here the structure of these AlphaFold-predicted human proteins for the presence of knots. We found that the human proteome contains 65 robustly knotted proteins, including the most complex type of a knot yet reported in proteins. That knot type, denoted 63 in mathematical notation, would necessitate a more complex folding path than any knotted proteins characterized to date. In some cases AlphaFold structure predictions are not highly accurate, which either makes their topology hard to verify or results in topological artifacts. Other structures that we found, which are knotted, potentially knotted, and structures with artifacts (knots) we deposited in a database available at: https://knotprot.cent.uw.edu.pl/alphafold.

Probing the structural, electronic and magnetic properties of AgnSc (n = 1–16) clusters

The structural, electronic and magnetic properties of AgnSc (n = 1–16) clusters have been studied on the basis of density functional theory and the CALYPSO structure prediction method.

Electronic structure and photocatalytic band offset of few-layer GeP2

Based on a sophisticated crystal structure prediction method, we propose two-dimensional (2D) GeP2in the tetragonal (T) phase never observed for other group IV–V compounds.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

Crystal structures of four new coumarin polymorphs were solved by crystal structure prediction method and their lattice and free energies were calculated by advanced techniques.

A database assisted protein structure prediction method via a swarm intelligence algorithm

A swarm-intelligence-based protein structure prediction method holds promise for narrowing the sequence-structure gap of proteins.