ArticleInternational journal of molecular sciences2023
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Determination of Structural Factors Contributing to Protection of Zinc Fingers in Estrogen Receptor α through Molecular Dynamic Simulations.The journal of physical chemistry. B · 2025Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
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4 authors.
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Abstract
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S
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