ArticleJournal of chemical information and modeling2023
Large-Scale Docking in the Cloud.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 23 citations in OpenAlex.
- Automated pharmacophore hypothesis generator for SILCS-Pharm: ph4gen.Journal of computer-aided molecular design · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Machine learning-guided QSAR screening of fluconazole analogs and FDA-approved drugs against Candida albicans, with docking, molecular dynamics, and ADMET analysis.Molecular diversity · 2026Article
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.Journal of chemical theory and computation · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Article
- Synthon-Based Strategies Exploiting Molecular Similarity and Protein-Ligand Interactions for Efficient Screening of Ultra-Large Chemical Libraries.Journal of chemical information and modeling · 2025Article
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- Identifying Artifacts from Large Library Docking.Journal of medicinal chemistry · 2024Article
- Identifying Artifacts from Large Library Docking.bioRxiv : the preprint server for biology · 2024Article
- Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking.Journal of chemical information and modeling · 2024Article
- DockOpt: A Tool for Automatic Optimization of Docking Models.Journal of chemical information and modeling · 2024Article
- HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra-large chemical libraries.Molecular informatics · 2024Article
- Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Molecular docking is a pragmatic approach to exploit protein structures for new ligand discovery, but the growing size of available chemical space is increasingly challenging to screen on in-house computer clusters. We have therefore developed AWS-DOCK, a protocol for running UCSF DOCK in the AWS cloud. Our approach leverages the low cost and scalability of cloud resources combined with a low-molecule-cost docking engine to screen billions of molecules efficiently. We benchmarked our system by screening 50 million HAC 22 molecules against the DRD4 receptor with an average CPU time of around 1 s per molecule. We saw up to 3-fold variations in cost between AWS availability zones. Docking 4.5 billion lead-like molecules, a 7 week calculation on our 1000-core lab cluster, runs in about a week depending on accessible CPUs, in AWS for around $25,000, less than the cost of two new nodes. The cloud docking protocol is described in easy-to-follow steps and may be sufficiently general to be used for other docking programs. All the tools to enable AWS-DOCK are available free to everyone, while DOCK 3.8 is free for academic research.
Indexed as
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.