ArticleJournal of computational chemistry2011
VoteDock: consensus docking method for prediction of protein-ligand interactions.
Article in Journal of computational chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Structural and Biological Evidence for Acetylcholinesterase-Targeted Insecticidal Activity in Musca domestica: A 4.5 Å Distance Correlation From Novel Benzenesulfonamide Derivatives.Molecular informatics · 2026Article
- New insights on Drug's design against candidiasis on the fructose biphosphate aldolase (Fba1) and the pyruvate kinase (Pk) ofBiochemistry and biophysics reports · 2025Article
- Multi-target Phenylpropanoids Against Epilepsy.Current neuropharmacology · 2024Review
- Identification and validation of a small molecule targeting ROR1 for the treatment of triple negative breast cancer.Frontiers in cell and developmental biology · 2023Article
- dockECR: Open consensus docking and ranking protocol for virtual screening of small molecules.Journal of molecular graphics & modelling · 2021Article
- Development of a caffeic acid-phthalimide hybrid compound for NADPH oxidase inhibition.RSC advances · 2021Article
- AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.PLoS computational biology · 2021Article
- Pharmacokinetics and drug-likeness of antidiabetic flavonoids: Molecular docking and DFT study.PloS one · 2021Article
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Application of MM-PBSA Methods in Virtual Screening.Molecules (Basel, Switzerland) · 2020Review
- ACID: a free tool for drug repurposing using consensus inverse docking strategy.Journal of cheminformatics · 2019Article
- Key Topics in Molecular Docking for Drug Design.International journal of molecular sciences · 2019Review
- Exponential consensus ranking improves the outcome in docking and receptor ensemble docking.Scientific reports · 2019Article
- Building a virtual ligand screening pipeline using free software: a survey.Briefings in bioinformatics · 2016Review
- vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available.Journal of cheminformatics · 2016Article
- Charting a Path to Success in Virtual Screening.Molecules (Basel, Switzerland) · 2015Review
- Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.Molecules (Basel, Switzerland) · 2014Review
- Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study.Journal of chemical information and modeling · 2014Article
- Computational methods in drug discovery.Pharmacological reviews · 2014Review
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Authors and funding
5 authors.
Funding
Abstract
Molecular recognition plays a fundamental role in all biological processes, and that is why great efforts have been made to understand and predict protein-ligand interactions. Finding a molecule that can potentially bind to a target protein is particularly essential in drug discovery and still remains an expensive and time-consuming task. In silico, tools are frequently used to screen molecular libraries to identify new lead compounds, and if protein structure is known, various protein-ligand docking programs can be used. The aim of docking procedure is to predict correct poses of ligand in the binding site of the protein as well as to score them according to the strength of interaction in a reasonable time frame. The purpose of our studies was to present the novel consensus approach to predict both protein-ligand complex structure and its corresponding binding affinity. Our method used as the input the results from seven docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) that are widely used for docking of ligands. We evaluated it on the extensive benchmark dataset of 1300 protein-ligands pairs from refined PDBbind database for which the structural and affinity data was available. We compared independently its ability of proper scoring and posing to the previously proposed methods. In most cases, our method is able to dock properly approximately 20% of pairs more than docking methods on average, and over 10% of pairs more than the best single program. The RMSD value of the predicted complex conformation versus its native one is reduced by a factor of 0.5 Å. Finally, we were able to increase the Pearson correlation of the predicted binding affinity in comparison with the experimental value up to 0.5.
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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.