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Protocols

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 citations

 (13)
call_split

Implication of Terminal Residues at Protein Protein and Protein DNA Interfaces

2016
PLoS One
PMCID: 5017611
PMID: 27611671
DOI: 10.1371/journal.pone.0162143
call_split See protocol

[…] evel, 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) and those extracted […]

library_books

Structural determinants of adhesion by Protocadherin 19 and implications for its role in epilepsy

2016
eLife
PMCID: 5115871
PMID: 27787195
DOI: 10.7554/eLife.18529.033

[…] re supplement 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 inte […]

library_books

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

2015
Bioinformatics
PMCID: 4743631
PMID: 26508758
DOI: 10.1093/bioinformatics/btv622

[…] estimation of interface stability. PISA is currently the most popular method for predicting biological assemblies. Additional details about PISA are described in the next section.A notable approach, NOXclass, appeared in 2006 and used six interface properties in a support vector machine three-state classifier distinguishing obligate, non-obligate and crystal packing interactions (). Another metho […]

library_books

Use B factor related features for accurate classification between protein binding interfaces and crystal packing contacts

2014
BMC Bioinformatics
PMCID: 4290652
PMID: 25522196
DOI: 10.1186/1471-2105-15-S16-S3

[…] mical 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 of interfa […]

library_books

Protein Protein Interface Detection Using the Energy Centrality Relationship (ECR) Characteristic of Proteins

2014
PLoS One
PMCID: 4022497
PMID: 24830938
DOI: 10.1371/journal.pone.0097115

[…] tion 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 database […]

library_books

The role of electrostatic energy in prediction of obligate protein protein interactions

2013
Proteome Sci
PMCID: 3907787
PMID: 24564955
DOI: 10.1186/1477-5956-11-S1-S11

[…] amino acid type features, which is much higher than the accuracy obtained by using six interface properties including interface area, interface area ratio, conservation score and gap volume index of NOXClass [] with 88.52% prediction accuracy (as reported by the authors), 46 solvent accessible and interface area properties of [] with 81.83% prediction accuracy, 210 features of solvent accessible […]


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

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