Protein-protein interactions are essential to all aspects of life. Specific interactions result from evolutionary pressure at the interacting interfaces of partner proteins. However, evolutionary pressure is not homogeneous ...

Overlapping genes exist in all domains of life and are especially abundant in viral genomes. The existence of overlapping reading frames increases the rising of deleterious mutations for one of the proteins, since a single ...

Background: A key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect ...

© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.Bacteriophages are the most abundant entity on the planet and play very relevant roles in the diversity and ...

Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for ...

Intrinsically disordered proteins/regions (IDPs/IDRs) are crucial components of the cell, they are highly abundant and participate ubiquitously in a wide range of biological functions, such as regulatory processes and cell ...

Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a network of co-evolving clusters of ...

Proteins' native structure is an ensemble of conformers in equilibrium, including all their respective functional states and intermediates. The induced-fit first and the pre-equilibrium theories later, described how ...