Gene evolution has long been thought to be primarily driven by duplication and
rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes …

How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …

Protein design aims to build novel proteins customized for specific purposes, thereby
holding the potential to tackle many environmental and biomedical problems. Recent …

We are now entering a new era in protein sequence and structure annotation, with hundreds
of millions of predicted protein structures made available through the AlphaFold database …

Abstract The MPI Bioinformatics Toolkit (http://toolkit. tuebingen. mpg. de) is an open,
interactive web service for comprehensive and collaborative protein bioinformatic analysis. It …

Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the
TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α) 8 …

Background Evolutionarily unrelated proteins that catalyze the same biochemical reactions
are often referred to as analogous-as opposed to homologous-enzymes. The existence of …

Abstract Domains are the structural, functional and evolutionary units of proteins. They
combine to form multidomain proteins. The evolutionary history of this molecular …

Abstract We present GenEra (https://github. com/josuebarrera/GenEra), a DIAMOND-fueled
gene-family founder inference framework that addresses previously raised limitations and …

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 …