Highlights•Coevolutionary modeling has an immense potential in structural systems
biology.•Interaction between two protein families can be detected.•Specific interaction …

Coevolutionary sequence analysis has become a commonly used technique for de novo
prediction of the structure and function of proteins, RNA, and protein complexes. We present …

Increasing numbers of protein interactions have been identified in high-throughput
experiments, but only a small proportion have solved structures. Recently, sequence …

Proteins have evolved to perform diverse cellular functions, from serving as reaction
catalysts to coordinating cellular propagation and development. Frequently, proteins do not …

AlphaFold-Multimer has greatly improved the protein complex structure prediction, but its
accuracy also depends on the quality of the multiple sequence alignment (MSA) formed by …

Ortholog protein complexes are responsible for equivalent functions in different organisms.
However, during evolution, each organism adapts to meet its physiological needs and the …

Abstract Knowledge of the detailed structure of macromolecular interactions is key to a better
understanding and modulation of essential cellular functions and pathological situations …

Motivation In the last decade, de novo protein structure prediction accuracy for individual
proteins has improved significantly by utilising deep learning (DL) methods for harvesting …

Selective pressures on protein-coding regions that provide fitness advantages can lead to
the regions' fixation and conservation in genome duplications and speciation events …

Protein–protein interactions (PPIs) play essential roles in most biological processes. The
binding interfaces between interacting proteins impose evolutionary constraints that have …