ArticleJournal of chemical information and modeling2013
Docking challenge: protein sampling and molecular docking performance.
Article in Journal of chemical information and modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 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
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.
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Who cites it
77 citing papers in PubMed, 277 citations in OpenAlex.
- Production of Anti-melanogenic Glucosides via Molecular Docking-guided Biotransformation of p-hydroxyphenethyl anisate.Applied biochemistry and biotechnology · 2026Article
- Cyclic Peptides as Modulators of Protein-Protein Interactions: A Survival Guide from Discovery Platforms to AI-Driven Design.International journal of molecular sciences · 2026Review
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Natural Products in Epilepsy Treatment: From Traditional Medicine Towards Computational Drug Discovery.Current issues in molecular biology · 2026Review
- In silico identification of sclerostin inhibitors.Molecular diversity · 2026Article
- Novel Heterocyclic Compounds Exhibit Potent Antileukemic Activity through Selective Induction of Apoptosis and HDAC8 Interaction in AML Cells.Anti-cancer agents in medicinal chemistry · 2026Article
- Towards Explainable Computational Toxicology: Linking Antitargets to Rodent Acute Toxicity.Pharmaceutics · 2025Article
- Evaluating the ciprofloxacin potentiation efficacy of repurposed drug flupentixol through efflux pump inhibition of pathogenic bacteria.Scientific reports · 2025Article
- Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input.bioRxiv : the preprint server for biology · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- Structure-Based Identification of Non-covalent Prolyl Oligopeptidase 80 Inhibitors TargetingJournal of chemical information and modeling · 2025Article
- Synthesis, X-Ray Structure, Characterization, Antifungal Activity, DFT, and Molecular Simulation of a Novel Pyrazole Carboxylic Acid.Current topics in medicinal chemistry · 2025Article
- Novel insights from comprehensive analysis: The role of cuproptosis and peripheral immune infiltration in Alzheimer's disease.PloS one · 2025Article
- Investigating the binding affinity, molecular dynamics, and ADMET properties of curcumin-IONPs as a mucoadhesive bioavailable oral treatment for iron deficiency anemia.Scientific reports · 2024Article
- Virtual Screening and Validation of Affinity DNA Functional Ligands for IgG Fc Segment.International journal of molecular sciences · 2024Article
- Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.Molecular diversity · 2024Article
- Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides.International journal of molecular sciences · 2024Article
- Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herbF1000Research · 2024Article
- Evaluation of novel compounds as anti-bacterial or anti-virulence agents.Frontiers in cellular and infection microbiology · 2024Review
- Sampling and Scoring in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Computational tools are essential in the drug design process, especially in order to take advantage of the increasing numbers of solved X-ray and NMR protein-ligand structures. Nowadays, molecular docking methods are routinely used for prediction of protein-ligand interactions and to aid in selecting potent molecules as a part of virtual screening of large databases. The improvements and advances in computational capacity in the past decade have allowed for further developments in molecular docking algorithms to address more complicated aspects such as protein flexibility. The effects of incorporation of active site water molecules and implicit or explicit solvation of the binding site are other relevant issues to be addressed in the docking procedures. Using the right docking algorithm at the right stage of virtual screening is most important. We report a staged study to address the effects of various aspects of protein flexibility and inclusion of active site water molecules on docking effectiveness to retrieve (and to be able to predict) correct ligand poses and to rank docked ligands in relation to their biological activity for CHK1, ERK2, LpxC, and UPA. We generated multiple conformers for the ligand and compared different docking algorithms that use a variety of approaches to protein flexibility, including rigid receptor, soft receptor, flexible side chains, induced fit, and multiple structure algorithms. Docking accuracy varied from 1% to 84%, demonstrating that the choice of method is important.
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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.