ArticleJournal of computer-aided molecular design2013
On homology modeling of the M₂ muscarinic acetylcholine receptor subtype.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Structure-guided discovery of a novel BTK inhibitor inducing apoptosis and G1 phase arrest in tumor cells.Molecular diversity · 2026Article
- Characterization of Plant-Derived Natural Inhibitors of Dipeptidyl Peptidase-4 as Potential Antidiabetic Agents: A Computational Study.Pharmaceutics · 2024Article
- Protective Effects of Rhamnetin in Carbapenem-ResistantInternational journal of molecular sciences · 2023Article
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- Fisetin 8-C-glucoside as entry inhibitor in SARS CoV-2 infection: molecular modelling study.Journal of biomolecular structure & dynamics · 2022Article
- Discovery of Histone Deacetylase Inhibitor Using Molecular Modeling and Free Energy Calculations.ACS omega · 2022Article
- Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (MScientific reports · 2021Article
- Article
- Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17).Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Twelve homology models of the human M2 muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M3 muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.
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