ReviewMolecular biotechnology2024
Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes.
Review in Molecular biotechnology, 2024. 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.
The trial behind it
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Who cites it
3 citing papers in PubMed.
- Hydrophobicity-Driven Disruption Mechanism in Kindlin-3 Induced by Leukocyte Adhesion Deficiency Mutation.ACS omega · 2025Article
- Elucidating multifaceted targets of Marein in cerebral ischemia-reperfusion injury.Frontiers in chemistry · 2025Article
- Network Pharmacology, Molecular Docking Analysis and Molecular Dynamics Simulation ofCurrent pharmaceutical design · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.
Indexed as
Identifiers
38374320What OpenQuestion holds
Registered trials
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