ArticleBioinformatics (Oxford, England)2019
AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- From Dynamics to Diagnosis and Therapy: A Multiscale Computational Framework for MALT1-Targeted Cancer Theranostics.Journal of chemical information and modeling · 2026Article
- Neuropharmacology of halogenated DMT analogs: psychoplastogenic and antidepressant properties of 5-Br-DMT, a psychedelic derivative with low hallucinogenic potential.Molecular psychiatry · 2026Article
- Mechanistic insights intoFood chemistry: X · 2026Article
- Predicting Protein-Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph.Interdisciplinary sciences, computational life sciences · 2025Article
- Omeprazole exacerbates intervertebral disc degeneration through Caspase-3 mediated apoptosis of nucleus pulposus cells: a Mendelian randomization, network toxicology, and in vitro experimental study.Journal of orthopaedic surgery and research · 2025Article
- Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?Journal of chemical information and modeling · 2025Article
- Exploring the potential of herbal drugs for treating liver fibrosis: a computational screening approach.Asian biomedicine : research, reviews and news · 2025Article
- Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance.Protein science : a publication of the Protein Society · 2025Article
- Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies.International journal of molecular sciences · 2025Article
- Allosteric modulation of Plasmodium falciparum Isoleucyl tRNA synthetase by South African natural compounds.PloS one · 2025Article
- In Vitro and Computational Response of Differential Catalysis byInternational journal of molecular sciences · 2024Article
- Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.Journal of chemical information and modeling · 2024Article
- Rational Design of Benzobisheterocycle Metallo-β-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes.Journal of medicinal chemistry · 2024Article
- Exploring the Mechanism of Zhishi-Xiebai-Guizhi Decoction for the Treatment of Hypoxic Pulmonary Hypertension based on Network Pharmacology and Experimental Analyses.Current pharmaceutical design · 2024Article
- Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery.Frontiers in microbiology · 2024Article
- Identification of a Pentasaccharide Lead Compound with High Affinity to the SARS-CoV-2 Spike Protein via In Silico Screening.International journal of molecular sciences · 2023Article
- A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.iScience · 2023Article
- Viral inhibitory potential of hyoscyamine in Japanese encephalitis virus-infected embryonated chicken eggs involving multiple signaling pathways.Archives of virology · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
summaryThe performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations. AVAILABILITY AND IMPLEMENTATION: AutoDock Bias is distributed with MGLTools (since version 1.5.7), and freely available on the web at http://ccsb.scripps.edu/mgltools/ or http://autodockbias.wordpress.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.