TranceptEVE: Combining family-specific and family-agnostic models of protein sequences for improved fitness prediction. Learning Meaningful Representations of Life Workshop, NeurIPS (2022). Lin, Z. et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science ...
Localization and function The names, ligands and functions of the 15 hormone recep- tors in family B1 are summarized in Table 1. As mentioned above, nine of the ligands are structurally related and three of the receptors respond selectively to different ligands that are all synthesized by post...
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Since there are multiple PDI family members, their functions may be overlapped. It has been shown that PDI family members may have at least one function as described here, whether it be as oxidases, reductases, isomerases, or molecular chaperones. The differences in structural determinants especi...
“Markov” matrix representing the transition probabilities between all pairs of vertices. As MCL is fast and scalable, it has been used for predicting protein family [61] and in a number of other domains. Pereira-Lealet al[62] transformed the protein interaction network into a line graph and...
The evolutionary history of UrtB and UrtC-like transporter permeases clearly contains numerous examples of paralogy formation and neofunctionalization, such that the protein family now contains examples of both ancient divergences with conserved function, and more modern splits with divergent function. By...
Protein kinase is a family of enzymes that catalyzes the transfer of a phosphate group from ATP to a protein or peptide substrate. This phosphorylation usually results in a functional change of the substrate and is among the most common mechanisms of cell signaling in both eukaryotes and prokaryot...
Although the precise role played by MAPK family members in normal GI epithelial cell physiology is largely undefined, data from variousin vitromodels suggest that they regulate the proliferation and differentiation responses of cell to growth factors andpeptide hormones. They also appear to funct...
This cluster of interacting proteins is also found in a third species, the Epstein-Barr virus EBV, which is of the same viral family as KSHV. Three of the four ORFs of the cluster in KSHV have sequence homologs in EBV, namely ORF23, ORF67.5, ORF29b. All of the corresponding ORFs in ...
Protein motif detection is key to identifying conserved protein domains within family of proteins as well as deducing its structure and function within the genome. The HMMER [1, 2] suite of programs is widely used for protein motif finding, building the profiled Hidden Markov Model (HMM), scan...