NOXclass

[…] 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) […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]