ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling

TL;DR

ESM All-Atom (ESM-AA) is a novel protein language model that unifies atom-level and residue-level molecular modeling, enabling enhanced understanding and application in protein engineering and protein-molecule tasks.

Contribution

The paper introduces ESM-AA, a multi-scale protein language model that operates at both atom and residue levels, overcoming previous limitations of residue-only models.

Findings

ESM-AA outperforms previous methods in protein-molecule tasks.

It captures relationships among residues and atoms effectively.

It retains protein understanding while gaining molecular knowledge.

Abstract

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins. The source codes of ESM-AA are publicly released at https://github.com/zhengkangjie/ESM-AA.