ArticleJournal of chemical theory and computation2021
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 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
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Who cites it
180 citing papers in PubMed, 359 citations in OpenAlex.
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- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Enhanced Line Search Improves Robustness and Efficiency of Pose Sampling in Protein-Ligand Docking.Journal of chemical theory and computation · 2026Article
- OXR1 is a dual redox-mitochondrial checkpoint governing osteoclast differentiation and bone loss in an osteoporosis mouse model.Nature communications · 2026Article
- Pushing the boundaries of virtual screening scale of combinatorial spaces with the V-SYNTHES approach.npj drug discovery · 2026Article
- AI-enhanced adaptive virtual screening of large libraries for ligand discovery.Nature biotechnology · 2026Article
- Redox and structural determinants of mitochondrial complex III inhibition by triphenylphosphonium-conjugated atovaquone analogs.Redox biology · 2026Article
- AI-Enforced Ultra-Large Virtual Screening Discovers Potent CD28 Binders.Journal of chemical information and modeling · 2026Article
- Dual Metabolic Targeting of Cancer: Lessons from Metformin and 2-Deoxy-D-Glucose Combinations.Cancers · 2026Article
- Article
- Benchmarking Docking Protocols on Predicting Alternative Binding Modes.Journal of chemical information and modeling · 2026Article
- SMASH: Screening Molecules Accurately on Small Hardware. Fast, user-friendly, enhanced with a machine learning virtual screening tool.Journal of molecular modeling · 2026Article
- Cytotoxic Activity ofInternational journal of molecular sciences · 2026Article
- KASSPer: kinase active site structure prediction using protein and ligand language models and its application to virtual screening.Bioinformatics (Oxford, England) · 2026Article
- Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.Nature protocols · 2026Review
- AI-Assisted Identification of a Putative Allosteric Ligand Targeting the CDK4/Cyclin D1 Protein-Protein Interface.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium.Nature communications · 2026Article
- DNA-Binding Properties of Iridium(III) Complexes Encompassing Design, Function and Biophysical Assessments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Review
120 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
AutoDock4 is a widely used program for docking small molecules to macromolecular targets. It describes ligand-receptor interactions using a physics-inspired scoring function that has been proven useful in a variety of drug discovery projects. However, compared to more modern and recent software, AutoDock4 has longer execution times, limiting its applicability to large scale dockings. To address this problem, we describe an OpenCL implementation of AutoDock4, called AutoDock-GPU, that leverages the highly parallel architecture of GPU hardware to reduce docking runtime by up to 350-fold with respect to a single-threaded process. Moreover, we introduce the gradient-based local search method ADADELTA, as well as an improved version of the Solis-Wets random optimizer from AutoDock4. These efficient local search algorithms significantly reduce the number of calls to the scoring function that are needed to produce good results. The improvements reported here, both in terms of docking throughput and search efficiency, facilitate the use of the AutoDock4 scoring function in large scale virtual screening.
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.