ArticleAntibiotics (Basel, Switzerland)2023
Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents.
Article in Antibiotics (Basel, Switzerland), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- Article
- Current Status and Perspectives of Antibacterial Agents Belonging to 2-Oxazolidinones.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Design, Synthesis and Biological Evaluation of New Oxazolidinone Antimicrobial Agents with Low Monoamine Oxidase A Inhibition.Drug design, development and therapy · 2026Article
- Aptamer-Engineered Ellipsometry for Clinical Detection of BALF-Derived Exosomes: Multi-Level Engineering for Prognostic Evaluation of Immunotherapy Responses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative in vitro and in silico evaluation of HSP60-derived peptides as immunomodulators of the TLR4/MD-2 complex.Scientific reports · 2025Article
- Synthesis and antibacterial activity of novel benzodioxin-containing oxazolidinones against M. abscessus.Bioorganic & medicinal chemistry letters · 2025Article
- Integrated Machine Learning and Structure-Based Virtual Screening Identifies Natural Product Targeting 50S Ribosome Inhibitory Activity AgainstMolecules (Basel, Switzerland) · 2025Article
- Phytochemical Characterization and Anti-Molecules (Basel, Switzerland) · 2025Article
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
- Alpha-Glucosidase Inhibition, Antioxidant Activities, and Molecular Docking Study of Krom Luang Chumphon Khet Udomsak, a Thai Traditional Remedy.Advances in pharmacological and pharmaceutical sciences · 2024Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular docking. It would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. We examined the performance of five molecular docking programs (AutoDock 4, AutoDock Vina, DOCK 6, rDock, and RLDock) for their ability to model ribosomal-ligand interactions with oxazolidinones. Eleven ribosomal crystal structures with oxazolidinones as the ligands were docked. The accuracy was evaluated by calculating the docked complexes' root-mean-square deviation (RMSD) and the program's internal scoring function. The rankings for each program based on the median RMSD between the native and predicted were DOCK 6 > AD4 > Vina > RDOCK >> RLDOCK. Results demonstrate that the top-performing program, DOCK 6, could accurately replicate the ligand binding in only four of the eleven ribosomes due to the poor electron density of said ribosomal structures. In this study, we have further benchmarked the performance of the DOCK 6 docking algorithm and scoring in improving virtual screening (VS) enrichment using the dataset of 285 oxazolidinone derivatives against oxazolidinone binding sites in the
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