ArticleStructure (London, England : 1993)2020
Structure-Based Analysis of Cryptic-Site Opening.
Article in Structure (London, England : 1993), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Fragment-Based Discovery of KLK6 and KLK7 Inhibitors.Journal of chemical information and modeling · 2026Article
- The influence of ligands on AlphaFold3 prediction of cryptic pockets.Communications biology · 2026Article
- Biophysical insights into a cryptic ligand site in the hydrophobic core of human PCNA.Biophysical journal · 2026Article
- CryptoBank: A resource for the identification and prediction of cryptic sites in proteins.Science advances · 2026Article
- Derivatives of the Cashew Nut Shell Liquid as Ligands ofACS omega · 2025Article
- Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.Journal of chemical information and modeling · 2025Article
- Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family.Molecular biology and evolution · 2025Article
- Recent computational advances in the identification of cryptic binding sites for drug discovery.Bioinformatics advances · 2025Review
- Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Which cryptic sites are feasible drug targets?Drug discovery today · 2024Review
- Protein Ensemble Generation Through Variational Autoencoder Latent Space Sampling.Journal of chemical theory and computation · 2024Article
- Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network.Nature communications · 2023Article
- FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.Journal of molecular biology · 2022Article
- Druggable Transient Pockets in Protein Kinases.Molecules (Basel, Switzerland) · 2021Review
- Spatiotemporal identification of druggable binding sites using deep learning.Communications biology · 2020Article
- AnalyzingFrontiers in molecular biosciences · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Many proteins in their unbound structures have cryptic sites that are not appropriately sized for drug binding. We consider here 32 proteins from the recently published CryptoSite set with validated cryptic sites, and study whether the sites remain cryptic in all available X-ray structures of the proteins solved without any ligand bound near the sites. It was shown that only few of these proteins have binding pockets that never form without ligand binding. Sites that are cryptic in some structures but spontaneously form in others are also rare. In most proteins the forming of pockets is affected by mutations or ligand binding at locations far from the cryptic site. To further explore these mechanisms, we applied adiabatic biased molecular dynamics simulations to guide the proteins from their ligand-free structures to ligand-bound conformations, and studied the distribution of druggability scores of the pockets located at the cryptic sites.
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