ArticleNucleic acids research2022
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 52 citations in OpenAlex.
- AI-Driven discovery and experimental validation of covalent FGFR4 inhibitors for hepatocellular carcinoma.Journal of translational medicine · 2026Article
- CHARMM-GUIbioRxiv : the preprint server for biology · 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
- Cheminformatic analysis of protein surfaces provides binding site insights and informs identification strategies.Future medicinal chemistry · 2025Article
- Article
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Illuminating the Druggable Human Proteome with an AI Protein Profiling Platform.Research square · 2025Article
- Illuminating the Druggable Human Proteome with an AI Protein Profiling Platform.bioRxiv : the preprint server for biology · 2025Article
- Computational Design of Lysine Targeting Covalent Binders Using Rosetta.Journal of chemical information and modeling · 2025Article
- Natural Language Processing Methods for the Study of Protein-Ligand Interactions.Journal of chemical information and modeling · 2025Review
- Article
- CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation.Journal of molecular biology · 2024Article
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines.JACS Au · 2024Article
- A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells.Chemical science · 2024Article
- Structure-Based Identification of Kelch-like ECH-Associated Protein 1 as a Pharmacological Target of Electrophile-Containing Catechol-ACS pharmacology & translational science · 2024Article
- Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp.JACS Au · 2024Article
- Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines.bioRxiv : the preprint server for biology · 2024Article
- Two-Step Covalent Docking with Attracting Cavities.Journal of chemical information and modeling · 2023Article
- Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices.Molecular diversity · 2023Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, the drug discovery paradigm has shifted toward compounds that covalently modify disease-associated target proteins, because they tend to possess high potency, selectivity, and duration of action. The rational design of novel targeted covalent inhibitors (TCIs) typically starts from resolved macromolecular structures of target proteins in their apo or holo forms. However, the existing TCI databases contain only a paucity of covalent protein-ligand (cP-L) complexes. Herein, we report CovPDB, the first database solely dedicated to high-resolution cocrystal structures of biologically relevant cP-L complexes, curated from the Protein Data Bank. For these curated complexes, the chemical structures and warheads of pre-reactive electrophilic ligands as well as the covalent bonding mechanisms to their target proteins were expertly manually annotated. Totally, CovPDB contains 733 proteins and 1,501 ligands, relating to 2,294 cP-L complexes, 93 reactive warheads, 14 targetable residues, and 21 covalent mechanisms. Users are provided with an intuitive and interactive web interface that allows multiple search and browsing options to explore the covalent interactome at a molecular level in order to develop novel TCIs. CovPDB is freely accessible at http://www.pharmbioinf.uni-freiburg.de/covpdb/ and its contents are available for download as flat files of various formats.
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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.