DiffPaSS-high-performance differentiable pairing of protein sequences using soft scores.

ABSTRACT:

Motivation

Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations in amino acid usage due to the need to maintain complementary interaction interfaces. Thus, the problem of finding interacting pairs can be formulated as searching for a pairing of sequences that maximizes a sequence similarity or a coevolution score. Several methods have been developed to address this problem, applying different approximate optimization methods to different scores.

Results

We introduce Differentiable Pairing using Soft Scores (DiffPaSS), a differentiable framework for flexible, fast, and hyperparameter-free

SUBMITTER: Lupo U 

PROVIDER: S-EPMC11676329 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature