Abstract Language models are playing an increasingly important role in many areas of
artificial intelligence (AI) and computational biology. In this primer, we discuss the ways in …

Sequence database searches followed by homology-based function transfer form one of the
oldest and most popular approaches for predicting protein functions, such as Gene Ontology …

Motivation Language models are routinely used for text classification and generative tasks.
Recently, the same architectures were applied to protein sequences, unlocking powerful …

Multiple sequence alignment (MSA) has evolved into a fundamental tool in the biological
sciences, playing a pivotal role in predicting molecular structures and functions. With broad …

Purpose Despite the many progresses with alignment algorithms, aligning divergent protein
sequences with less than 20–35% pairwise identity (so called" twilight zone") remains a …

Protein circular permutations are crucial for understanding protein evolution and
functionality. Traditional detection methods face challenges: sequence-based approaches …

Proteins are involved in a variety of functions in living organisms. The mutation of amino acid
residues in a protein alters its structure, stability, binding, and function, with some mutations …

Motivation For the alignment of large numbers of protein sequences, tools are predominant
that decide to align two residues using only simple prior knowledge, eg amino acid …

Human Leukocyte Antigen (HLA) is like a device that monitors the internal environment of
the body. T lymphocytes immediately recognize the HLA molecules that are expressed on …

Duplication is an essential evolutionary mechanism that operates at the scale of
chromosomes, large chunks of DNA sequences, genes, protein domains, and shorter motifs …