ArticleScientific reports2024
Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- In silico discovery of natural and synthetic inhibitors targeting AKT1 in prostate cancer.Molecular diversity · 2026Article
- TGF-β inhibitor SB431542 suppresses SARS-CoV-2 replication through multistep inhibition.Journal of virology · 2025Article
- Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins.Nucleic acids research · 2025Article
- Semi-rational engineering of an α-L-fucosidase for regioselective synthesis of fucosyl-Food chemistry. Molecular sciences · 2025Article
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6 authors.
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Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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