BACKGROUND: Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which more than two identical protein...
IEEE/ACM transactions on computational biology and bioinformatics
31940546
Protein-Protein Interactions (PPIs) play an irreplaceable role in biological activities of organisms. Although many high-throughput methods are used to identify PPIs from different kinds of organisms, they have some shortcomings, such as high cost an...
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing...
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
During starvation in the yeast vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and...
Evolution-based deep generative models represent an exciting direction in understanding and designing proteins. An open question is whether such models can learn specialized functional constraints that control fitness in specific biological contexts....
Epigenetic inheritance of heterochromatin requires transfer of parental H3-H4 tetramers to both daughter duplexes during replication. Three recent papers exploit yeast genetics coupled to inheritance assays and AlphaFold2-multimer predictions coupled...
Proteins interact with each other in complex ways to perform significant biological functions. These interactions, known as protein-protein interactions (PPIs), can be depicted as a graph where proteins are nodes and their interactions are edges. The...
The prion phenotype in yeast manifests as a white, pink, or red color pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to exhibit (red) sectored phenotypes within otherwise completely white colonies. Further inve...
Chromatin remodeling complexes, such as the Saccharomyces cerevisiae INO80 complex, exemplify how dynamic protein interaction networks govern cellular function through a balance of conserved structural modules and context-dependent functional partner...