ArticleACS omega2024
PROTAC-Design-Evaluator (PRODE): An Advanced Method for In-Silico PROTAC Design.
Article in ACS omega, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed, 10 citations in OpenAlex.
- Artificial intelligence empowers targeted protein degradation: Core technological innovations, multi-scenario applications, and translational prospects.Smart molecules : open access · 2026Review
- Computational mapping of productive POI-E3 ligase conformations to guide de novo degrader design: application to WEE1 and PKMYT1 PROTACs.Journal of cheminformatics · 2026Article
- Bellerophon: An Automated Tool for PROTAC Decomposition.ACS medicinal chemistry letters · 2026Article
- Molecular Glues Stabilize Water-Mediated Hydrogen Bonds in Ternary Complexes.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Data-Driven Generation of Conformational Ensembles and Ternary Complexes for PROTAC and Other Chimera Systems.Journal of chemical information and modeling · 2025Article
- AI-DPAPT: a machine learning framework for predicting PROTAC activity.Molecular diversity · 2025Article
- Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design.ACS omega · 2025Article
- Standards for Computational Methods in Drug Design and Discovery: Simplified Guidance for Authors and Reviewers.Drug design, development and therapy · 2025Article
- Circular RNA in hepatocellular carcinoma: emerging therapeutic strategies.Frontiers in immunology · 2025Review
- The Applications of Computational Tools in PROTAC Development.Current topics in medicinal chemistry · 2025Review
- Precision oncology revolution: CRISPR-Cas9 and PROTAC technologies unleashed.Frontiers in genetics · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PROTAC (proteolysis-targeting chimeras) is a rapidly evolving technology to target undruggable targets. The mechanism by which this happens is when a bifunctional molecule binds to a target protein and also brings an E3 ubiquitin ligase in proximity to trigger ubiquitination and degradation of the target protein. Yet, in-silico-driven approaches to design these heterobifunctional molecules that have the desired functional properties to induce proximity between the target protein and E3 ligase remain to be established. In this paper, we present a novel in-silico method for PROTAC design and to demonstrate the validity of our approach, we show that for a BRD4-VHL-PROTAC-mediated ternary complex known in the literature, we are able to reproduce the PROTAC binding mode, the structure of the ternary complex formed therein, and the free energy (Δ
Identifiers
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.