Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.

ABSTRACT: Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (AF), this study computationally examines the entire UniProt database to create a robust dataset of knotted and unknotted proteins. Utilizing this dataset, we develop a machine learning (ML) model capable of accurately predicting the presence of knots in protein structures solely from their amino acid sequences. We tested the model's capabilities on 100 proteins whose structures had not yet been predicted by AF and found agreement with our local prediction in 92% cases. From the point of view of structural biology, we found that all potentially k

SUBMITTER: Sikora M 

PROVIDER: S-EPMC11184937 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature