ArticleJournal of medicinal chemistry2022
In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses.
Article in Journal of medicinal chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- From Ternary Modeling to Predictive PROTAC Design: A Computational Perspective.Journal of chemical information and modeling · 2026Article
- Metastable Protein-Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1-VHL System.JACS Au · 2026Article
- Quantum Mechanics-Based Ranking of Predicted Proteolysis Targeting Chimeras-Mediated Ternary Complexes.ACS medicinal chemistry letters · 2025Article
- Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design.ACS omega · 2025Article
- MEGA PROTAC, MEGA DOCK-based PROTAC mediated ternary complex formation pipeline with sequential filtering and rank aggregation.Scientific reports · 2025Article
- Standards for Computational Methods in Drug Design and Discovery: Simplified Guidance for Authors and Reviewers.Drug design, development and therapy · 2025Article
- The Applications of Computational Tools in PROTAC Development.Current topics in medicinal chemistry · 2025Review
- StreaMD: the toolkit for high-throughput molecular dynamics simulations.Journal of cheminformatics · 2024Article
- DiffPROTACs is a deep learning-based generator for proteolysis targeting chimeras.Briefings in bioinformatics · 2024Article
- Article
- DegraderTCM: A Computationally Sparing Approach for Predicting Ternary Degradation Complexes.ACS medicinal chemistry letters · 2024Article
- Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development.Pharmaceuticals (Basel, Switzerland) · 2023Review
- A platform for the rapid synthesis of molecular glues (Rapid-Glue) under miniaturized conditions for direct biological screening.European journal of medicinal chemistry · 2023Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation.Journal of medicinal chemistry · 2023Article
- Targeted Protein Degradation for Infectious Diseases: from Basic Biology to Drug Discovery.ACS bio & med chem Au · 2023Review
- Targeted protein degradation as an antiviral approach.Antiviral research · 2023Article
- Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods.The journal of physical chemistry. B · 2023Article
- The importance of controls in targeted protein degradation: Determining mechanism.Methods in enzymology · 2023Article
- Computer aided drug design in the development of proteolysis targeting chimeras.Computational and structural biotechnology journal · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC-induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on the pose occupancy time in MD, where native poses exhibit longer occupancy times at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by classic MM/GBSA. A specific heating scheme is then applied to accelerate ternary pose departure, with the pose occupancy time and fraction being measured. This scoring identifies the native pose in all systems tested. Its success is partially attributed to the dynamic nature of pose departure analyses, which accounts for entropic effects typically neglected in the faster static scoring methods, while entropy plays a greater role in protein-protein than in protein-ligand systems.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.