NOXclass

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]