Structure-Informed Protein Language Model
Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie Lozano Payel Das Jian Tang
Protein language models are a powerful tool for learning protein
representations through pre-training on vast protein sequence datasets.
However, traditional protein language models lack explicit structural
supervision, despite its relevance to protein function. To address this issue,
we introduce the integration of remote homology detection to distill structural
information into protein language models without requiring explicit protein
structures as input. We evaluate the impact of this structure-informed training
on downstream protein function prediction tasks. Experimental results reveal
consistent improvements in function annotation accuracy for EC number and GO
term prediction. Performance on mutant datasets, however, varies based on the
relationship between targeted properties and protein structures. This
underscores the importance of considering this relationship when applying
structure-aware training to protein function prediction tasks. Code and model
weights are available at https://github.com/DeepGraphLearning/esm-s.