ArticleACS medicinal chemistry letters2019
Coupling Supervised Molecular Dynamics (SuMD) with Entropy Estimations To Shine Light on the Stability of Multiple Binding Sites.
Article in ACS medicinal chemistry letters, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed, 6 citations in OpenAlex.
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies.Molecules (Basel, Switzerland) · 2023Review
- Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.NAR genomics and bioinformatics · 2022Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exploring at the molecular level, all possible ligand-protein approaching pathways and, consequently, identifying the energetically favorable binding sites is considered crucial to depict a clear picture of the whole scenario of ligand-protein binding. In fact, a ligand can recognize a protein in multiple binding sites, adopting multiple conformations in every single binding site and inducing protein modifications upon binding. In the present work, we would like to present how it is possible to couple a supervised molecular dynamics (SuMD) approach to explore, from an unbound state, the most energetically favorable recognition pathways of the ligand to its protein, with an enthalpic and entropic characterization of the most stable ligand-protein bound states, using the protein kinase CK2α as a prototype study. We identified two accessory binding pockets surrounding the ATP-binding site having a strong enthalpic contribution but a different configurational entropy contribution, suggesting that they play a different role.
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Registered trials
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