NOXclass specifications

Information


Unique identifier OMICS_09516
Name NOXclass
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two protein protomers, which refer to the two polypeptide chains in the protein complex, to NOXclass. Either a PDB identifier with two chain names, or two PDB files containing the two protomer structure models have to be specified to NOXclass.
Operating system Unix/Linux
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained No

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Information


Unique identifier OMICS_09516
Name NOXclass
Interface Web user interface
Restrictions to use None
Input data Two protein protomers, which refer to the two polypeptide chains in the protein complex, to NOXclass. Either a PDB identifier with two chain names, or two PDB files containing the two protomer structure models have to be specified to NOXclass.
Programming languages Python
Computer skills Basic
Stability Stable
Maintained No

Publication for NOXclass

NOXclass in publications

 (8)
PMCID: 5017611
PMID: 27611671
DOI: 10.1371/journal.pone.0162143

[…] at the 70% threshold. we termed this list dimer70. in this list, interfaces are already annotated in terms of:, heterodimer or homodimer complexes,, obligate or non-obligate complexes (predicted by noxclass []),, biological interfaces or crystal contacts (predicted by noxclass)., we further made the distinction between interfaces extracted from complexes with two chains (dimers) […]

PMCID: 5115871
PMID: 27787195
DOI: 10.7554/eLife.18529.033

[…] 2., 10.7554/elife.18529.012figure 2—figure supplement 3., analysis of the pcdh19-i1 antiparallel interface with the protein interfaces, surfaces and assemblies (pisa) server () and with the noxclass classifier () revealed a large interface (~1650 å2), that is unlikely to be a crystal packing artifact (89.21% biological, 81% obligate). in contrast, the possible antiparallel pcdh19-i2 […]

PMCID: 4572935
PMID: 26370141
DOI: 10.1038/srep14214

[…] potential of mean force to distinguish biological from crystal packing contacts for protein homodimers and monomers. in 2006, zhu et al. integrated six interface properties and implemented them as noxclass to discriminate between obligate, non-obligate and crystal packing interactions. tsuchiya et al. constructed a server, called prebi, to predict biological interfaces in protein crystal […]

PMCID: 4290652
PMID: 25522196
DOI: 10.1186/1471-2105-15-S16-S3

[…] complementarity []. zhu et al. [] have extracted six properties from interfaces, such as interface size, amino acid composition and gap volume, and then used them as an svm input to train their noxclass classifier to discriminate between crystal packing, obligate and non-obligate interactions []. recently, capitani's group [] have proposed to use core size and evolutionary metrics […]

PMCID: 4022497
PMID: 24830938
DOI: 10.1371/journal.pone.0097115

[…] to other features to identify macromolecular complexes in solution . even with these enhanced analyses, the relationship of the complex with function may still be problematic. for example, pisa, noxclass, and eppic servers all identify actin:dnase as the likely biounit –. as a result, the ability to distinguish flip from func, though improved, remains obscure. while large interactome […]


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NOXclass institution(s)
Max-Planck-lnstitut für Informatik, Saarbrücken, Germany

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