Jointly Embedding Protein Structures and Sequences through Residue Level Alignment.

ABSTRACT: The relationships between protein sequences, structures, and functions are determined by complex codes that scientists aim to decipher. While structures contain key information about proteins' biochemical functions, they are often experimentally difficult to obtain. In contrast, protein sequences are abundant but are a step removed from function. In this paper, we propose residue level alignment (RLA)-a self-supervised objective for aligning sequence and structure embedding spaces. By situating sequence and structure encoders within the same latent space, RLA enriches the sequence encoder with spatial information. Moreover, our framework enables us to measure the similarity between a sequence and structure by comparing their RLA embeddings. We show how RLA similarity scores can be used for

SUBMITTER: Birnbaum F 

PROVIDER: S-EPMC12490763 | biostudies-literature | 2024 Nov-Dec

REPOSITORIES: biostudies-literature