ArticleActa crystallographica. Section D, Biological crystallography2014
Deformable elastic network refinement for low-resolution macromolecular crystallography.
Article in Acta crystallographica. Section D, Biological crystallography, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Improved structure of mouse gasdermin D: a new blueprint for structure-based drug design.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Structural Impact of Ex Vivo Resistance Mutations on HIV-1 Integrase Polymers Induced by Allosteric Inhibitors.Journal of molecular biology · 2025Article
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- Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.Acta crystallographica. Section D, Structural biology · 2023Article
- Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization.PLoS pathogens · 2023Article
- Improving sampling of crystallographic disorder in ensemble refinement.Acta crystallographica. Section D, Structural biology · 2021Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Structural insights into Fe-S protein biogenesis by the CIA targeting complex.Nature structural & molecular biology · 2020Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
- Structural basis for λN-dependent processive transcription antitermination.Nature microbiology · 2017Article
- Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.Cell cycle (Georgetown, Tex.) · 2017Article
- Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.PLoS biology · 2016Article
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- Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.Annual review of biophysics · 2016Review
- Tackling the crystallographic structure determination of the COP9 signalosome.Acta crystallographica. Section D, Structural biology · 2016Article
- Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.Nature · 2015Article
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3 authors.
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Abstract
Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.
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