ArticlePLoS computational biology2014
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- From Genome Inspection to Precision Agrochemicals: A Structure-Based Antivirulence Roadmap for Sustainable Crop Protection againstJournal of agricultural and food chemistry · 2026Review
- Oral bioavailability property prediction based on task similarity transfer learning.Molecular diversity · 2026Article
- A Twist of Fate: The Helix-Turn-Helix Motif inJournal of chemical information and modeling · 2025Article
- The comprehensive SARS-CoV-2 'hijackome' knowledge base.Cell discovery · 2024Article
- SiteFerret: Beyond Simple Pocket Identification in Proteins.Journal of chemical theory and computation · 2023Article
- Mechanism of Phellodendron and Anemarrhena Drug Pair on the Treatment of Liver Cancer Based on Network Pharmacology and Bioinformatics.Frontiers in oncology · 2022Article
- On modeling and utilizing chemical compound information with deep learning technologies: A task-oriented approach.Computational and structural biotechnology journal · 2022Review
- Review
- Druggability and drug-likeness concepts in drug design: are biomodelling and predictive tools having their say?Journal of molecular modeling · 2020Review
- Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations.Protein science : a publication of the Protein Society · 2020Article
- A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology.Handbook of experimental pharmacology · 2019Article
- Structure-guided Discovery of Dual-recognition Chemibodies.Scientific reports · 2018Article
- Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future.International journal of molecular sciences · 2016Review
- CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.Journal of molecular biology · 2016Article
- Flexibility and small pockets at protein-protein interfaces: New insights into druggability.Progress in biophysics and molecular biology · 2015Review
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.
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