ArticleBioinformatics (Oxford, England)2023
Predicting allosteric pockets in protein biological assemblages.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Integrated multi-omics identifies lineage-dependent myeloid cells recruitment and the APP-CD74 axis as an immunoregulatory target in pediatric high-grade glioma.Acta neuropathologica · 2026Article
- The allosteric landscape of the Src kinase.Science advances · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- A Twist of Fate: The Helix-Turn-Helix Motif inJournal of chemical information and modeling · 2025Article
- Resistance to Allosteric Inhibitors.Journal of molecular biology · 2025Review
- AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools.ACS omega · 2025Article
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody.eLife · 2025Article
- Global hinge sites of proteins as target sites for drug binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery.Signal transduction and targeted therapy · 2024Review
- Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.The Journal of chemical physics · 2023Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
motivationAllostery enables changes to the dynamic behavior of a protein at distant positions induced by binding. Here, we present APOP, a new allosteric pocket prediction method, which perturbs the pockets formed in the structure by stiffening pairwise interactions in the elastic network across the pocket, to emulate ligand binding. Ranking the pockets based on the shifts in the global mode frequencies, as well as their mean local hydrophobicities, leads to high prediction success when tested on a dataset of allosteric proteins, composed of both monomers and multimeric assemblages.
resultsOut of the 104 test cases, APOP predicts known allosteric pockets for 92 within the top 3 rank out of multiple pockets available in the protein. In addition, we demonstrate that APOP can also find new alternative allosteric pockets in proteins. Particularly interesting findings are the discovery of previously overlooked large pockets located in the centers of many protein biological assemblages; binding of ligands at these sites would likely be particularly effective in changing the protein's global dynamics. AVAILABILITY AND IMPLEMENTATION: APOP is freely available as an open-source code (https://github.com/Ambuj-UF/APOP) and as a web server at https://apop.bb.iastate.edu/.
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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.