Restraint Quality, Not Quantity, Predicts Peptide–Protein Docking Outcomes

Understanding protein-peptide interactions is essential for uncovering cellular signaling mechanisms and advancing therapeutic development, as these interactions play central roles in numerous biological processes. Gaining structural insight into such complexes is crucial, yet traditional methods like nuclear magnetic resonance (NMR) and X-ray crystallography are often time-consuming and experimentally demanding. Computational approachesincluding physics-based docking and deep-learning (DL) structure predictors such as AlphaFold3, Boltz-2, and Chai-1offer powerful alternatives. Accurately modeling flexible peptides that bind to shallow, surface-exposed regions remains difficult for physics-based methods, and although multiple sequence alignment-driven DL models can achieve excellent performance in well-behaved systems, they too can struggle when the peptide adopts noncanonical conformations or when sequence identity is low. In such cases, distance restraints are often required to guide the docking toward accurate and biologically meaningful solutions, yet acquiring multiple high-quality restraints is often difficult. To address the limitation of physics and DL approaches, we developed a restraint scoring function that integrates evolutionary conservation, spatial proximity, and geometric distribution to assess the informativeness of restraint sets. This enables a more accurate evaluation of docking inputs and overcomes the shortcomings of relying solely on restraint count. Building on this framework, we introduce a minimal-restraint docking strategy, capable of identifying optimized subsets of restraints that lead to high-quality structural models. We evaluate a comprehensive set of protein–peptide systems, including 43 SH3 domain complexes, 8 WW domain complexes, and 19 medium-difficulty cases from the PepPCBench benchmark. Our approach shows that model quality improves as the restraint score increases, supporting restraint score as a simple, interpretable indicator of docking success. We further identify clear, domain-specific restraint-score thresholds for the SH3 and WW systems that enable accurate model selection. Together, these results offer a scalable and efficient strategy for structure prediction in data-limited contexts and lay the groundwork for restraint-informed modeling with quantifiable confidence, as well as a powerful foundation for data-efficient machine learning-based peptide–protein docking.