Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

Deep neural-network-based language models (LMs) are increasingly applied to large-scale
protein sequence data to predict protein function. However, being largely black-box models …

Computational methods for protein structure modelling are routinely used to complement
experimental structure determination, thus they help to address a broad spectrum of …

The seemingly limitless diversity of proteins in nature arose from only a few thousand
domain prototypes, but the origin of these themselves has remained unclear. We are …

Natural recombination combines pieces of preexisting proteins to create new tertiary
structures and functions. We describe a computational protocol, called SEWING, which is …

The accuracy of sequence‐based tertiary contact predictions was assessed in a blind
prediction experiment at the CASP13 meeting. After 4 years of significant improvements in …

The vast majority of theoretically possible polypeptide chains do not fold, let alone confer
function. Hence, protein evolution from preexisting building blocks has clear potential …

Proteins share similar segments with one another. Such “reused parts”—which have been
successfully incorporated into other proteins—are likely to offer an evolutionary advantage …

Here, we systematically decompose the known protein structural universe into its basic
elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone …

The high frequency of internal structural symmetry in common protein folds is presumed to
reflect their evolutionary origins from the repetition and fusion of ancient peptide modules …