ReviewMolecules (Basel, Switzerland)2014
Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.
Review in Molecules (Basel, Switzerland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Artificial intelligence-driven discovery of coumarin-based therapeutics: Revolutionizing target identification and validation.Pharmaceutical science advances · 2026Review
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
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- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 2026Article
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- A Novel Weighted Ensemble Framework of Transformer and Deep Q-Network for ATP-Binding Site Prediction Using Protein Language Model Features.International journal of molecular sciences · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- Microbial enzymes for plastic degradation: a comprehensive review of current status and emerging trends.Biodegradation · 2026Review
- Molegro Virtual Docker for Docking Screens.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploring the Potential of Dolutegravir in Alzheimer's Disease Treatment: Insights from Network Pharmacology andCentral nervous system agents in medicinal chemistry · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
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- Multimodal out-of-distribution individual uncertainty quantification enhances binding affinity prediction for polypharmacology.Nature machine intelligence · 2025Article
- Quercetin and Its Structural Analogs as NUDT5 Inhibitors: A Preliminary In Silico Study.International journal of molecular sciences · 2025Article
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- Computational investigation of antiviral peptide interactions with Mpox DNA polymerase.In silico pharmacology · 2025Article
- Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling.Journal of chemical information and modeling · 2024Article
- In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance.PNAS nexus · 2024Article
27 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.
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