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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


No version available

Maintainer


  • person_outline Mario Albrecht <>

Publication for RINalyzer

RINalyzer citations

 (12)
library_books

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

2018
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 […]

library_books

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

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

[…] 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
PMCID: 5371819
PMID: 28358005
DOI: 10.1038/srep45389

[…] 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 […]

library_books

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

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

[…] between the remote conformational changes and the hyperactivity of mutant enzymes., to further analyze differences observed by hdx, we focused on the perturbed regions in crystal structures. using rinalyzer [], we examined residue interaction networks in the wild type and the studied mutants. this analysis revealed that most differences observed with hdx could be explained by conformational […]

library_books

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

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

[…] for constructing the interactive residue interaction network (rin) by using cytoscape 3.2.1., 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., alignment of the wild type complex with the mutant complex […]

library_books

The RING 2.0 web server for high quality residue interaction networks

2016
PMCID: 4987896
PMID: 27198219
DOI: 10.1093/nar/gkw315

[…] folding, intra protein domain–domain communication and catalytic activity (–). on the other hand, software generating rins still has limitations due to the use of simplified interaction types. rinalyzer () for example calculates only hydrogen bond, van der waals (vdw) and generic contacts based on distance. this limitation can be explained by technical reasons, such as the computational […]


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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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