ArticleJournal of chemical information and modeling2022
Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.Journal of chemical information and modeling · 2025Article
- Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases.Journal of chemical information and modeling · 2024Article
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4 authors.
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Abstract
Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits and pitfalls. Results obtained for both crystal structures and molecular dynamics (MD) simulations were analyzed to investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential for the low-diameter tunnel description, and assessment of the tunnel functionality based only on their geometrical parameters is challenging. We showed that the small-molecule tracking approach can provide a detailed description of the system; however, it can also be the most computationally demanding.
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