RINalyzer statistics

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Citations per year

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

This map represents all the scientific publications referring to RINalyzer per scientific context
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RINalyzer specifications

Information


Unique identifier OMICS_16860
Name RINalyzer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Versioning


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Maintainer


  • person_outline Mario Albrecht

Publication for RINalyzer

RINalyzer citations

 (15)
library_books

Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region

2018
Sci Rep
PMCID: 5772511
PMID: 29343701
DOI: 10.1038/s41598-017-19075-2

[…] The representative structure for each system (wild-type and alanine mutants) was submitted to RING server. The network was visualized and analyzed using RINalyzer and StructureViz module of Cytoscapev3.5.1. In protein-ligand 3D graph, nodes represented residues and edges symbolized different type of interactions such as van der Waals, ionic interactio […]

library_books

Genetic identification and molecular modeling characterization reveal a novel PROM1 mutation in Stargardt4 like macular dystrophy

2017
Oncotarget
PMCID: 5787432
PMID: 29416601
DOI: 10.18632/oncotarget.22343

[…] odes in the pathway. All the processed residues (functional extracellular domain of PROM1 in position 179-433) were separately imported into Cytoscape 3.3.0 to reconstruct amino acidic networks using RINalyzer plug-in software []. Therefore, the Cytoscape archive files were constructed by submitting the crystal structure of both the wild type and the mutant protein to RING server []. […]

library_books

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

2017
Sci Rep
PMCID: 5371819
PMID: 28358005
DOI: 10.1038/srep45389

[…] e rotary molecular motor.To elucidate critical contacts mediating interactions between the CD or linker domain (LD) and the PBD, the FpPPDK conformational intermediate was analyzed with Cytoscape and RINalyzer, which identified a salt bridge formed between E804 and R462, and non-polar patches at I864 in the PBD and L378 in the LD likely involved in hydrophobic interactions. Both interactions may r […]

library_books

Structure Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

2017
Sci Rep
PMCID: 5341570
PMID: 28272553
DOI: 10.1038/srep43807

[…] . Correlation-weighted degree, which is the summation of strengths of all the edges connected to a given node, indicates the importance of the node. After construction of the network, Cytoscape3.4.0, RINalyzer, and NetworkAnalyzer were used to calculate the topological parameters of the network. The shortest path between any two nodes in the network was identified using the Floyd-Warshall algorith […]

library_books

Oligomeric interface modulation causes misregulation of purine 5´ nucleotidase in relapsed leukemia

2016
BMC Biol
PMCID: 5070119
PMID: 27756303
DOI: 10.1186/s12915-016-0313-y

[…] nal file . The protein structures were analyzed using software included in the CCP4 package [], namely PISA [], LSQKAB [], and BAVERAGE. In addition, the residue interaction network was assessed with RINalyzer []. Structural models were visualized using PyMOL software (DeLano Scientific). Missing loops were modeled using the ModLoop server [] to illustrate the possible position of these regions in […]

library_books

Structural insights into conformational stability of both wild type and mutant EZH2 receptor

2016
Sci Rep
PMCID: 5054529
PMID: 27713574
DOI: 10.1038/srep34984

[…] Visualization of the network generated by the RING server was observed in Cytoscape using the plugin RINalyzer. The edges such as hydrogen bonds, salt bridges, and van der Waal interactions are labelled based on the type of interaction. […]


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RINalyzer institution(s)
Max Planck Institute for Informatics, Saarbrucken, Germany; TU Dortmund University, Dortmund, Germany
RINalyzer funding source(s)
This study was financially supported by the German National Genome Research Network (NGFN) and by the German Research Foundation (DFG), contract number KFO 129/1-2.

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