Gene

Signal peptide

The Internet

Sorting

Web server

Algorithm

Machine learning

World Wide Web

Protein subcellular localization prediction

Membrane protein

Artificial intelligence

Peptide sequence

Protein function prediction

Subcellular localization

Interpretability

Protein Sorting Signals

Protein function

Computer science

Membrane

Proteomics

Genetics

Protein targeting

Bioinformatics

Computational biology

Biology

Nucleic Acids Research

The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction and improvements in both performance and interpretability. For training and validation, we curate eukaryotic and human multi-location protein datasets with stringent homology partitioning and enriched with sorting signal information compiled from the literature. We achieve state-of-the-art performance in DeepLoc 2.0 by using a pre-trained protein language model. It has the further advantage that it uses sequence input rather than relying on slower protein profiles. We provide two means of better interpretability: an attention output along the sequence and highly accurate prediction of nine different types of protein sorting signals. We find that the attention output correlates well with the position of sorting signals. The webserver is available at services.healthtech.dtu.dk/service.php?DeepLoc-2.0.

DeepLoc 2.0: multi-label subcellular localization prediction using protein language models