KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program

By Vincent B. Chen, Ian W. Davis, David C Richardson. 2009

177 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “The KiNG Java-based viewer (Chen et al., 2009) set up by phenix.kinemage displays all model-validation outliers in 3D to highlight local clusters of outliers around single serious problems.”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “Images were generated using KiNG (Chen et al., 2009). overlap is just below the cutoff of 0.4 Å, resulting in the lower clashscore.”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “C dihedral with a red trapezoid, similar to their representations in Coot (Emsley & Cowtan, 2004) and KiNG (Chen et al., 2009); twisted peptide bonds (not shown) are similarly filled in yellow.”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “In the Richardson group, independent implementations of high-dimensional visualization features in two kinemage programs KiNG 250 and Mage 251 ultimately lead to a “ more general-purpose and more powerful ” implementation.”
MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “7 illustrates such a correction process in KiNG, rebuilding a backward-fitted leucine with a clash and a bad rotamer (one of the cases of a systematic error), resulting in an ideal geometry side chain with an excellent rotamer and well packed all-atom contacts.”
Graphical tools for macromolecular crystallography in PHENIX (2012, methodology): “Interactive model validation summaries (‘kinemages’) may also be loaded in KiNG (Chen et al. , 2009), providing visual validation similar to that available in MolProbity .”
Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design (2012, background): “( 36 – 38 The atomic overlap is shown with yellow and red dots, DNA is black, side chains are cyan, and the protein backbone is brown.”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, methodology): “To visualize interactions for the residue of interest, all-atom contacts were displayed in KiNG [39].”
MolProbity: More and better reference data for improved all‐atom structure validation (2018, methodology): “12,57 Its structure modeling and corrections, docking construction, image and movie creation, and of course interactive display can still be done offline by us and others, but Java is nearly dead for the important online display in MolProbity.”
EMPeror: a tool for visualizing high-throughput microbial community data (2013, methodology): “The main features that EMPeror provides are: (1) easily change visibility features of data points in the plots based on metadata; (2) can be easily embedded into other tools, such as Evident [16] as a reusable visualization component; (3) scale to thousands of points with minimal load times (seconds”
Model validation: local diagnosis, correction and when to quit (2018, methodology): “The backrub correction can be directly controlled in the KiNG graphics and modeling program (Chen et al., 2009; Richardson & Headd, 2012), providing a better understanding of how it works within the automated side-chain rebuilding in Coot or PHENIX.”