Adapting language models to protein sequences spawned the development of powerful
protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein …

Viral glycoproteins drive membrane fusion in enveloped viruses and determine host range,
tissue tropism and pathogenesis. Despite their importance, there is a fragmentary …

Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence
proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast …

Protein structure is conserved beyond sequence, making multiple structural alignment
(MSTA) essential for analyzing distantly related proteins. Computational prediction methods …

Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements
that we first identified in human gut metatranscriptomic data.“Obelisks” share several …

The processes of nutrient uptake and signal sensing are crucial for microbial survival and
adaptation. Membrane-embedded proteins involved in these functions (transporters and …

Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for
inferring evolutionary relationships, which has illuminated the evolutionary histories of …

The analysis of single-copy core genes, common to most members of a clade, is important
for key tasks in biology including phylogenetic reconstruction and assessing genome …

The rotation of the bacterial flagellum is powered by the MotAB stator complex, which
converts ion flux into torque. The origin and evolution of this remarkable complex is …

Structural divergence varies among protein residues. Unlike the classic problem of
substitution rate variation, this structural divergence variation has been largely ignored. Here …