Towards automated crystallographic structure refinement with phenix.refine
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Summary
This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
- Type
- article
- Published
- 2012-03-16
- Cited by
- 5,071
- References
- 152
- Access
- Open access
- OpenAlex
- https://openalex.org/W2154197653
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:5522673
Keywords
Suite, Computer science, Automation, Software suite, Graphical user interface
References
- The Protein Data Bank: a computer-based archival file for macromolecular structures.
- International Tables for X-Ray Crystallography
- International tables for crystallography
- On the derivation of dynamic information from diffraction data.
- Evolving Methods for Macromolecular Crystallography
- International tables for X-ray crystallography
- Experience with various techniques for the refinement of protein structures.
- Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures.
- TNT refinement package.
- The Bijvoet-difference Fourier synthesis.
- Stereochemically restrained refinement of macromolecular structures.
- SHELXL: high-resolution refinement.
- Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution.
- Macromolecular crystal twinning, lattice disorders and multiple crystals
- Protein crystallography at subatomic resolution
- Experimental assessment of differences between related protein crystal structures.
- The structure of N2 at 49 kbar and 299 K
- Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
- Simulated-annealing real-space refinement as a tool in model building.
- Crystallographic R Factor Refinement by Molecular Dynamics
Cited by
- Detection of alternative conformations by unrestrained refinement.
- Structural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1.
- Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector
- Vibriocholerae cytolysin recognizes the heptasaccharide core of complex N-glycans with nanomolar affinity
- Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
- 3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops.
- Structural characterization of the pulmonary innate immune protein SPLUNC1 and identification of lipid ligands
- Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator‐dependent tRNA modification
- How pH Modulates the Dimer-Decamer Interconversion of 2-Cys Peroxiredoxins from the Prx1 Subfamily*
- Thiosulfate Dehydrogenase (TsdA) from Allochromatium vinosum
- Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain.
- Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1
- Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia.
- Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module
- Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine
- Characterization of the Adeno-Associated Virus 1 and 6 Sialic Acid Binding Site
- Measuring and modeling diffuse scattering in protein X-ray crystallography
- Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa.
- Crystal structure of human PCNA in complex with the PIP box of DVC1.
- Structural and functional characterization of a highly stable endo-β-1,4-xylanase from Fusarium oxysporum and its development as an efficient immobilized biocatalyst
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