ArticleNucleic acids research2026
CB-Dock3: an enhanced web server for protein-ligand blind docking.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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
2 citing papers in PubMed.
- Neuroprotective Potential ofBiomolecules · 2026Article
- Multi-Omics-Guided Discovery ofMarine drugs · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Elucidating protein-ligand interactions is pivotal for understanding biological mechanisms and accelerating drug discovery. Blind docking, which identifies binding sites without prior knowledge, has become an indispensable computational strategy for analyzing the surge of protein structures generated by Cryo-EM and AI-based prediction tools like AlphaFold3. Our previous server, CB-Dock2, has been widely adopted by the global research community, averaging over 1000 daily submissions since July 2022 due to its accuracy and user-friendliness. Building on this foundation and incorporating extensive user feedback, we present CB-Dock3, a substantially enhanced platform. Key upgrades include a refined docking engine, an expanded template library, and support for diverse file formats. Benchmark evaluations on CASF-2016 demonstrate that CB-Dock3 achieves a success rate of 67.4% (RMSD ≤ 2.0 Å), representing a 10.6 percentage-point absolute improvement over its predecessor and outperforming other popular blind docking tools. Additionally, CB-Dock3 introduces critical new features driven by community needs: support for user-defined docking regions to handle large complexes, and a metal-aware protocol that explicitly retains essential metal ions and cofactors during simulation. CB-Dock3 stands as an accurate, rapid, and accessible resource for the scientific community, freely available at https://cadd.labshare.cn/cb-dock3/.
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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.