PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings.

ABSTRACT:

Motivation

Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.

Results

We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence threshold

SUBMITTER: Gonzales MEM 

PROVIDER: S-EPMC11783280 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature