Related Experiment Video
Updated: May 5, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
Bi-factor analysis based on noise-reduction (BIFANR): a new algorithm for detecting coevolving amino acid sites in
Juntao Liu1, Xiaoyun Duan, Jianyang Sun
1School of Mathematics, Shandong University, Jinan, China.
Abstract:
Previous statistical analyses have shown that amino acid sites in a protein evolve in a correlated way instead of independently. Even though located distantly in the linear sequence, the coevolved amino acids could be spatially adjacent in the tertiary structure, and constitute specific protein sectors. Moreover, these protein sectors are independent of one another in structure, function, and even evolution. Thus, systematic studies on protein sectors inside a protein will contribute to the clarification of protein function. In this paper, we propose a new algorithm BIFANR (Bi-factor Analysis Based on Noise-reduction) for detecting protein sectors in amino acid sequences. After applying BIFANR on S1A family and PDZ family, we carried out internal correlation test, statistical independence test, evolutionary rate analysis, evolutionary independence analysis, and function analysis to assess the prediction. The results showed that the amino acids in certain predicted protein sector are closely correlated in structure, function, and evolution, while protein sectors are nearly statistically independent. The results also indicated that the protein sectors have distinct evolutionary directions. In addition, compared with other algorithms, BIFANR has higher accuracy and robustness under the influence of noise sites.
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
Conservation of Protein Domains
Protein-protein Interfaces
Protein Folding Quality Check in the RER
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

