GapTrick-structural characterization of protein-protein interactions using AlphaFold.

ABSTRACT:

Motivation

The structural characterization of protein-protein interactions is a key step in understanding the functions of living cells. Here, I show that AlphaFold3 often fails to predict protein complexes that are either weak or dependent on the presence of a cofactor that is not included in a prediction.

Results

To address this problem, I developed gapTrick, an AlphaFold2-based approach that uses multimeric templates to improve prediction reliability. I demonstrate that gapTrick improves predictions of weak and incomplete complexes based on low-accuracy templates, such as individual protein models that have been rigid-body fitted into cryo-EM reconstructions. I also show that gapTrick identifies residue-residue interactions with high precision. These interaction predictio

SUBMITTER: Chojnowski G 

PROVIDER: S-EPMC12479393 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature