ArticleMolecules (Basel, Switzerland)2019
Systematic Studies on the Protocol and Criteria for Selecting a Covalent Docking Tool.
Article in Molecules (Basel, Switzerland), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 37 citations in OpenAlex.
- Single-Sequence Deep Learning Delivers Crystal-Quality Models of Covalent K-Ras G12 Hotspot Complexes.IUBMB life · 2026Article
- Benchmarking co-folding methods to predict the structures of covalent protein-ligand complexes.Acta pharmacologica Sinica · 2026Article
- Discovery of Covalent Ligands with AlphaFold3.Journal of the American Chemical Society · 2026Article
- Hybrid quantum/classical docking of covalent and non-covalent ligands with Attracting Cavities.Scientific reports · 2025Article
- Covalent Docking to the Active Sites of Thiamine Diphosphate-Dependent Enzymes.Molecules (Basel, Switzerland) · 2025Article
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Two-Step Covalent Docking with Attracting Cavities.Journal of chemical information and modeling · 2023Article
- In Silico Analysis of USP7 Inhibitors Based on Building QSAR Models and Fragment Design for Screening Marine Compound Libraries.Marine drugs · 2023Article
- A flexible data-free framework for structure-basedChemical science · 2023Article
- Analysis of the Chemical Composition and Evaluation of the Antioxidant, Antimicrobial, Anticoagulant, and Antidiabetic Properties ofBiomedicines · 2023Article
- Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices.Molecular diversity · 2023Review
- Potent VEGFR-2 inhibitors for resistant breast cancer: a comprehensive 3D-QSAR, ADMET, molecular docking and MMPBSA calculation on triazolopyrazine derivatives.Frontiers in molecular biosciences · 2023Article
- Advanced approaches of developing targeted covalent drugs.RSC medicinal chemistry · 2022Review
- Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery.Pharmaceuticals (Basel, Switzerland) · 2022Review
- Systematic Tracing of Susceptible Animals to SARS-CoV-2 by a Bioinformatics Framework.Frontiers in microbiology · 2022Article
- 10 years into the resurgence of covalent drugs.Future medicinal chemistry · 2021Article
- Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors.Trends in pharmacological sciences · 2020Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
With the resurgence of drugs with covalent binding mechanisms, much attention has been paid to docking methods for the discovery of targeted covalent inhibitors. The existence of many available covalent docking tools has inspired development of a systematic and objective procedure and criteria with which to evaluate these programs. In order to find a tool appropriate to studies of a covalently binding system, protocols and criteria are proposed for protein-ligand covalent docking studies. This paper consists of three sections: (1) curating a standard data set to evaluate covalent docking tools objectively; (2) establishing criteria to measure the performance of a tool applied for docking ligands into a complex system; and (3) creating a protocol to evaluate and select covalent binding tools. The protocols were applied to evaluate four covalent docking tools (MOE, GOLD, CovDock, and ICM-Pro) and parameters affecting covalent docking performance were investigated.
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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.