ArticleJournal of computer-aided molecular design2016
1001 Ways to run AutoDock Vina for virtual screening.
Article in Journal of computer-aided molecular design, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- "Therapeutic potential of Acalypha indica L. leaf fractions against foodborne pathogens: an in vitro and in silico study".Scientific reports · 2025Article
- Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.Discover oncology · 2025Article
- Computational exploration in search for novel natural product-derived EZH2 inhibitors for advancing anti-cancer therapy.Molecular diversity · 2025Article
- Comprehensive pan-cancer analysis of p62 reveals its contribution to shaping tumor microenvironment and anti-tumor immunity.Discover oncology · 2025Article
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- Pinene-Based Chiral Bipyridine Ligands Drive Potent Antibacterial Activity in Rhenium(I) Complexes.Molecules (Basel, Switzerland) · 2025Article
- A novel one-pot microwave assisted green synthesis of pyridinyl-1,3,5-triazine-2,4-diamine hybrids as potent antimicrobial agents.BMC chemistry · 2025Article
- Cytotoxicity evaluation and metabolomic profiling of Spheciospongia vagabunda-associated fungi corroborated by in silico studies.Scientific reports · 2025Article
- Repurposing FDA-approved drugs to find a novel inhibitor of alpha-ketoglutarate-dependent dioxygenase FTO to treat esophageal cancer.Research in pharmaceutical sciences · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-performance computing (HPC) infrastructures, and understand the impact of the choices made. Here, we review such considerations for a specific tool, AutoDock Vina, and use experimental data to illustrate the following points: (1) an additional level of parallelization increases virtual screening throughput on a multi-core machine; (2) capturing of the random seed is not enough (though necessary) for reproducibility on heterogeneous distributed computing systems; (3) the overall time spent on the screening of a ligand library can be improved by analysis of factors affecting execution time per ligand, including number of active torsions, heavy atoms and exhaustiveness. We also illustrate differences among four common HPC infrastructures: grid, Hadoop, small cluster and multi-core (virtual machine on the cloud). Our analysis shows that these platforms are suitable for screening experiments of different sizes. These considerations can guide scientists when choosing the best computing platform and set-up for their future large virtual screening experiments.
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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.