A Review of Current Computational Tools for Peptide–Protein Docking

Abstract

Peptide–protein docking is an increasingly important technique in computational biochemistry and drug discovery, allowing researchers to predict interactions between peptides and proteins and guiding the development of peptide-based therapeutics. This review provides a detailed overview of the current landscape of peptide–protein docking programs, emphasizing their importance and versatility. Through an extensive literature search, we identify and describe 14 dedicated peptide–protein docking programs, along with small-molecule docking software that supports peptide docking. Additionally, we explore state-of-the-art AI-driven alternatives that are advancing the field. By describing the distinct features, methodological approaches, strengths, and inherent limitations of each docking tool, this review aims to support researchers in navigating the wide range of available docking programs and making well-informed choices tailored to their specific research objectives.