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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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Maintainer


  • person_outline Mario Albrecht <>

Publication for RINalyzer

RINalyzer in publications

 (12)
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 […]

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 []., […]

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 […]

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 […]

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 […]


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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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