ArticleJournal of cheminformatics2023
EasyDock: customizable and scalable docking tool.
Article in Journal of cheminformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- SMILES2Docking: An Open-Source Desktop Workflow for Ligand Ionization, Stereochemistry-Aware Preparation and Semi-Empirical 3D Refinement.Molecular informatics · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.Journal of chemical information and modeling · 2026Article
- MBind: A Web-Based Platform for Metalloprotein and Nonmetalloprotein Docking with Optional ML Docking Integration.Molecules (Basel, Switzerland) · 2026Article
- ScrambleBench: a workflow for comparative assessment of structure-based de novo generative models.Journal of cheminformatics · 2026Article
- SMASH: Screening Molecules Accurately on Small Hardware. Fast, user-friendly, enhanced with a machine learning virtual screening tool.Journal of molecular modeling · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- CReM-pharm: de novo 3D pharmacophore-based design with synthetic accessibility awareness.Journal of cheminformatics · 2026Article
- Computational identification of epifriedelanol and derived analogs from Mikania cordata as potential HMG-CoA reductase inhibitors.PloS one · 2026Article
- Identification of stigmasterol derived AChE inhibitors for Alzheimer's disease using high throughput virtual screening and molecular dynamics simulations.Scientific reports · 2025Article
- Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity.Current medicinal chemistry · 2025Review
- In silico investigation of Toxicodendron succedaneum phytochemicals as extracellular signal-regulated kinase 2 inhibitors for non-small cell lung cancer therapy.Medical oncology (Northwood, London, England) · 2025Article
- Virtual screening,Toxicology reports · 2025Article
- Adenocarpine, Marmesin, and Lycocernuine from Ficus benjamina as Promising Inhibitors of Aldose Reductase in Diabetes: A Bioinformatics-Guided Approach.Applied biochemistry and biotechnology · 2025Article
- M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures.BMC bioinformatics · 2025Article
- Transcytosis-Driven Treatment of Neurodegenerative Disorders by mRNA-Expressed Antibody-Transferrin Conjugates.Biomedicines · 2024Review
- Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular docking. To facilitate these processes, there is a need for automated tools capable of efficiently docking a large number of molecules using multiple computational nodes within a reasonable timeframe. These tools should also allow for easy integration of new docking programs and provide a user-friendly program interface to support the development of further approaches utilizing docking as a foundation. Currently available tools have certain limitations, such as lacking a convenient program interface or lacking support for distributed computations. In response to these limitations, we have developed a module called EasyDock. It can be deployed over a network of computational nodes using the Dask library, without requiring a specific cluster scheduler. Furthermore, we have proposed and implemented a simple model that predicts the runtime of docking experiments and applied it to minimize overall docking time. The current version of EasyDock supports popular docking programs, namely Autodock Vina, gnina, and smina. Additionally, we implemented a supplementary feature to enable docking of boron-containing compounds, which are not inherently supported by Vina and smina, and demonstrated its applicability on a set of 55 PDB protein-ligand complexes.
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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.