CYRANGE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CYRANGE
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Tool usage distribution map

This map represents all the scientific publications referring to CYRANGE per scientific context
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Protocols

CYRANGE specifications

Information


Unique identifier OMICS_30661
Name CYRANGE
Interface Web user interface
Restrictions to use None
Input data Some cartesian coordinates of two or more structures.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Peter Guntert

Publication for CYRANGE

CYRANGE citations

 (5)
library_books

Structural and functional dissection of the DH and PH domains of oncogenic Bcr Abl tyrosine kinase

2017
Nat Commun
PMCID: 5727386
PMID: 29235475
DOI: 10.1038/s41467-017-02313-6

[…] ergy minimization in explicit solvent against the AMBER force field with OPALp–. RMSD values were calculated for the well-defined regions of the protein, residues 496–619, 638–693, as determined with CYRANGE.The interaction studies with the GTPases were done using a uniformly 15N-labeled DH domain at a concentration of 50 μM. GTPase stock solutions ranged between 600 and 900 μM. All proteins were […]

library_books

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists

2017
Comput Struct Biotechnol J
PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] condary structures in the determined structures. The automated identification of the ordered region of the determined structures is also possible using particular programs, e.g., NMRCORE , FindCore , CYRANGE and FitRobot . The resulting structural ensemble can be graphically represented using molecular viewers such as UCSF Chimera , CCP4mg , VMD-XPLOR , PyMol (https://www.pymol.org/) and MOLMOL . […]

library_books

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD NMR 2013

2015
J Biomol NMR
PMCID: 4569658
PMID: 26071966
DOI: 10.1007/s10858-015-9953-4

[…] recommended that the data for ill-defined regions should be part of the deposited dataset, but should not be included in the validation analysis (Montelione et al. ). It also recommended the program CyRange (Kirchner and Guentert ) as a robust tool for determining the well-defined and ill-defined regions. Following this recommendation, we established the well-defined regions for the ten targets ( […]

library_books

Analysis of the structural quality of the CASD NMR 2013 entries

2015
J Biomol NMR
PMCID: 4569653
PMID: 26032236
DOI: 10.1007/s10858-015-9949-0

[…] lues are calculated as follows. For each of the M conformers in the query ensemble, the RMSD between the backbone N, Cα and C’ atoms in the well-defined region of the reference ensemble as defined by CyRange (Kirchner and Guentert ) (see Table ) of each of the N conformers in the target ensemble is calculated, yielding a list of M × N RMSD values (or M(M-1)2 values for convergence calculations whe […]

call_split

Effects of NMR Spectral Resolution on Protein Structure Calculation

2013
PLoS One
PMCID: 3713035
PMID: 23874675
DOI: 10.1371/journal.pone.0068567
call_split See protocol

[…] k (BMRB) . The corresponding three-dimensional protein structures were obtained from the Protein Data Bank (PDB) . The optimal amino acid residue ranges for the PDB structures were obtained using the CYRANGE program for maintaining consistency in reporting RMSD values of calculated atomic coordinates. From the 400 initially selected protein structures, nineteen proteins structures, for which opti […]


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CYRANGE institution(s)
Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany; Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany; Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
CYRANGE funding source(s)
Supported by the Lichtenberg program of the Volkswagen Foundation and by a Grant-in-Aid for Scientific Research of the Japan Society for the Promotion of Science (JSPS).

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