ArticleJournal of chemical information and modeling2022
CovBinderInPDB: A Structure-Based Covalent Binder Database.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- 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
- Leak Proof PDBBind: A Reorganized Data Set of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction.The journal of physical chemistry. B · 2026Article
- Article
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening.Acta pharmaceutica Sinica. B · 2025Article
- 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
- A workflow to create a high-quality protein-ligand binding dataset for training, validation, and prediction tasks.Digital discovery · 2025Article
- MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling.Acta pharmacologica Sinica · 2025Article
- Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem.Journal of chemical information and modeling · 2025Article
- Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors.Molecules (Basel, Switzerland) · 2025Article
- Article
- Normalized Protein-Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening.Journal of chemical information and modeling · 2025Article
- CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation.Journal of molecular biology · 2024Article
- Two-Step Covalent Docking with Attracting Cavities.Journal of chemical information and modeling · 2023Article
- SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.Journal of chemical information and modeling · 2023Article
- Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation.Journal of chemical theory and computation · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Covalent inhibition has emerged as a promising orthogonal approach for drug discovery, despite the significant challenge in achieving target specificity. To facilitate the structure-based rational design of target-specific covalent modulators, we developed an integrated computational protocol to curate covalent binders from the RCSB Protein Data Bank (PDB). Starting from the macromolecular crystallographic information files (mmCIF) in the PDB archive, covalent bond records, which indicate the side chain modification of amino acid residue by a covalent binder, were collected and cleaned. Then, residue-binder adducts, which are products of chemical reactions between targeted residues and covalent binders, were recovered with the help of the Chemical Component Dictionary in PDB. Finally, several strategies were employed to curate the pre-reaction forms of covalent binders from the adducts. Our curated CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains. This database would set a solid foundation for developing and benchmarking computational strategies for covalent modulator design and is freely accessible at https://yzhang.hpc.nyu.edu/CovBinderInPDB.
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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.