The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms

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The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
The ModFOLD4 server for the quality assessment of 3D protein models (2013, methodology): “To calibrate the P-values, we used a similar approach to that previously adopted for measuring the coverage of genomic scale fold recognition (22,23).”
Identification and distribution of protein families in 120 completed genomes using Gene3D (2005, methodology): “GenTHREADER(27) applies threading algorithms to fold recognition in the absence of any detectable sequence similarity and has recently been used to construct the Genomic Threading Database.(28) Here we present the results of a novel protocol PFscape (Protein Family Landscape) that has been developed”
The ModFOLD server for the quality assessment of protein structural models (2008, methodology): “ModFOLD was shown to be competitive with clustering methods and significantly outperformed the individual MQAPs tested ( McGuffin, 2007 ).”