ArticleJournal of chemical information and modeling2025
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Targeted degradation of protein in hematologic malignancies: mechanisms, therapeutic strategies, and clinical prospects.Cancer gene therapy · 2026Review
- Artificial intelligence empowers targeted protein degradation: Core technological innovations, multi-scenario applications, and translational prospects.Smart molecules : open access · 2026Review
- COMPASS: A Computational Pipeline to Identify Linkers Predicting Ubiquitinable PROTAC-Induced Ternary Complexes.ChemMedChem · 2026Article
- A quantitative approach for defining the degradability landscape of protein degraders.Nature communications · 2026Article
- PROTAC-mediated regulation of programmed cell death: From molecular mechanisms to therapeutic breakthroughs.Innovation (Cambridge (Mass.)) · 2026Review
- A nanobody-based proteolysis-targeting chimera offers broad-spectrum protection against diverse influenza virus infections.Signal transduction and targeted therapy · 2026Article
- Folded-state compatibility and unfolded-state constraint govern staple-based stabilization: guidelines from a coiled-coil model.RSC chemical biology · 2026Article
- Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial Intelligence.The journal of physical chemistry letters · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that recruit E3 ubiquitin ligases to a target protein and induce its ubiquitination by forming a ternary complex. However, the structural dynamics underlying the complex formation and degradation efficiency remain unclear. In this study, we attempted an extensive conformational search using the parallel cascade selection molecular dynamics (PaCS-MD) and outlier flooding (OFLOOD) method for PROTACs differing in linker length. Markov state models revealed that while all PROTACs share a common low free-energy state, their structural distribution profiles differ significantly. These results suggest that linker-dependent conformational distribution profiles modulate degradation activity and cooperativity, offering mechanistic insights into rational PROTAC design.
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Registered trials
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