ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2014
A practical implicit solvent potential for NMR structure calculation.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- Mechanism of negative membrane curvature generation by I-BAR domains.Structure (London, England : 1993) · 2021Article
- Dynamic NaeLife · 2021Article
- Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State.Frontiers in molecular biosciences · 2021Article
- Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation.Nucleic acids research · 2020Article
- Structural Basis of Oligomerization of N-Terminal Domain of Spider Aciniform Silk Protein.International journal of molecular sciences · 2020Article
- The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.The Journal of biological chemistry · 2019Article
- Validation of protein backbone structures calculated from NMR angular restraints using Rosetta.Journal of biomolecular NMR · 2019Article
- Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel.Nature communications · 2019Article
- Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70.PloS one · 2019Article
- Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.Cell reports · 2018Article
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Authors and funding
4 authors.
Funding
Abstract
The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide templates. Here we describe a new implicit solvation potential, EEFx (Effective Energy Function for XPLOR-NIH), for NMR-restrained structure calculations of proteins in XPLOR-NIH. The key components of EEFx are an energy term for solvation energy that works together with other nonbonded energy functions, and a dedicated force field for conformational and nonbonded protein interaction parameters. The initial results obtained with EEFx show that significant improvements in structural quality can be obtained. EEFx is computationally efficient and can be used both to fold and refine structures. Overall, EEFx improves the quality of protein conformation and nonbonded atomic interactions. Moreover, such benefits are accompanied by enhanced structural precision and enhanced structural accuracy, reflected in improved agreement with the cross-validated dipolar coupling data. Finally, implementation of EEFx calculations is straightforward and computationally efficient. Overall, EEFx provides a useful method for the practical calculation of experimental protein structures in a physically realistic environment.
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