ArticleBioinformatics (Oxford, England)2011
Prediction of peptides binding to the PKA RIIalpha subunit using a hierarchical strategy.
Article in Bioinformatics (Oxford, England), 2011. 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, 67 citations in OpenAlex.
- Regulation of Translation by PKA Signaling Pathway.International journal of molecular sciences · 2026Review
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- LRBA is essential for urinary concentration and body water homeostasis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Targeting the actin nucleation promoting factor WASp provides a therapeutic approach for hematopoietic malignancies.Nature communications · 2021Article
- Inverse in silico-in vitro fishing of unexpected paroxetine kinase targets from tumor druggable kinome.Journal of molecular modeling · 2020Article
- Theoretical Studies on the Selectivity Mechanisms of Glycogen Synthase Kinase 3β (GSK3β) with Pyrazine ATP-competitive Inhibitors by 3DQSAR, Molecular Docking, Molecular Dynamics Simulation and Free Energy Calculations.Current computer-aided drug design · 2020Article
- Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation.Journal of molecular modeling · 2019Article
- HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.Nucleic acids research · 2019Article
- Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type IFrontiers in pharmacology · 2019Article
- Exploring the binding mechanisms of PDE5 with chromeno[2,3-RSC advances · 2018Article
- Discovery and Identification of Pyrazolopyramidine Analogs as Novel Potent Androgen Receptor Antagonists.Frontiers in pharmacology · 2018Article
- Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-IACS central science · 2017Article
- A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells.Nature communications · 2017Article
- In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Selection Strategy in Selecting Virtual Screening Candidates.Scientific reports · 2016Article
- Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation.PloS one · 2015Article
- Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain.Journal of proteome research · 2013Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationFavorable interaction between the regulatory subunit of the cAMP-dependent protein kinase (PKA) and a peptide in A-kinase anchoring proteins (AKAPs) is critical for translocating PKA to the subcellular sites where the enzyme phosphorylates its substrates. It is very hard to identify AKAPs peptides binding to PKA due to the high sequence diversity of AKAPs.
resultsWe propose a hierarchical and efficient approach, which combines molecular dynamics (MD) simulations, free energy calculations, virtual mutagenesis (VM) and bioinformatics analyses, to predict peptides binding to the PKA RIIα regulatory subunit in the human proteome systematically. Our approach successfully retrieved 15 out of 18 documented RIIα-binding peptides. Literature curation supported that many newly predicted peptides might be true AKAPs. Here, we present the first systematic search for AKAP peptides in the human proteome, which is useful to further experimental identification of AKAPs and functional analysis of their biological roles.
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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.