Work

Protein–Peptide Docking with ESMFold Language Model

Year: 2025

Type: article

Abstract: Designing peptide therapeutics requires precise peptide docking, which remains a challenge. We assessed the ESMFold language model, originally designed for protein structure prediction, for its effectiveness in protein-peptide docking. Various docking strategies, including polyglycine linkers and sampling-enhancing modifications, were explored. The number of acceptable-quality models among top-ranking results is comparable to traditional methods and generally lower than AlphaFold-Multimer or Alphafold 3, though ESMFold surpasses it in some cases. The combination of result quality and computational efficiency underscores ESMFold's potential value as a component in a consensus approach for high-throughput peptide design.

Source: Journal of Chemical Theory and Computation

DOI: 10.1021/acs.jctc.4c01585

Authors: Mateusz Zalewski, Björn Wallner, Sebastian Kmiecik

Institutions: University of Warsaw, Linköping University

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $4,500

Funder: Narodowe Centrum Nauki