VERIFY3D: assessment of protein models with three-dimensional profiles.

By D. Eisenberg, R. Lüthy, J. Bowie. 1997

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The Victor/FRST Function for Model Quality Estimation (2005, unknown): “…RAPDF (Samudrala et al. , 1998), AKBP (Lu et al. , 2001), DFIRE (Zhou et al. , 2002; Zhang et al. , 2004), SNAPP (Krishnamoorthy et al. , 2003), Errat (Colovos et al. , 1993), Prosa II (Sippl, 1993b), Verify3D (Luthy et al. , 1992; Eisenberg et al. , 1997), and ProQ (Wallner et al. , 2003).”
Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study (2020, methodology): “Various types of software were used to judge the validity of the model, such as PROCHECK [35], Verify 3D [36], PROVE [37], and ERRAT [38], in addition to the Ramachandran plot of the MolProbity web server.”
Can correct protein models be identified? (2003, methodology): “ProQ-LG has the highest correlation on the two independent measures, CA3 and Contact; whereas ProQ-MX does not perform as well as ProQ-LG, but still better than Prosa II, Verify3D, and Errat Besides ProQ, Prosa II shows correlations with LGscore and MaxSub comparable to the networks trained on a sin”
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12 (2018, methodology): “The following computational tools were available for download and have been installed and used locally on the CAMEO server: Dfire (Version 1.1)[31], Prosa 2003[29], ProQ2[32] and Verify3d[33].”
Evaluating the usefulness of protein structure models for molecular replacement (2005, methodology): “Unfortunately, the available quality evaluation measures, such as those provided by Verify3d (Eisenberg et al., 1997), Whatcheck (Hooft et al., 1996) and Procheck (Laskowski et al., 1993) do not correlate with the ability of the models to reconstruct the experimental structure (data not shown).”
Modeling and Docking Studies on Novel Mutants (K71L and T204V) of the ATPase Domain of Human Heat Shock 70 kDa Protein 1 (2014, methodology): “Validation of generated models was further performed by ProQ [24], ERRAT [25], Verify 3D [26] and ProSA [27] programs.”
Protein knot server: detection of knots in protein structures (2007, methodology): “Moreover, widely used protein structure veriﬁcation tools like WHATIF (18), VERIFY3D (19) and PROCHECK (20) do not have the capability to detect knots.”
Anti-HCV, nucleotide inhibitors, repurposing against COVID-19 (2020, unknown): “The program used to judge the validity of the model are PROCHECK [38], Verify 3D [39], PROVE [40], and ERRAT [41] in addition to the Ramachandran plot of the Molprobity.”
The ModFOLD4 server for the quality assessment of 3D protein models (2013, methodology): “Traditionally, statistically derived energy functions, such as ProSA (5) and DFIRE (6), have been used along with the alternative knowledge-based approaches, such as VERIFY3D (7), to provide single scores that relate to the global quality of protein models.”
Identification of correct regions in protein models using structural, alignment, and consensus information (2006, methodology): “Currently, three, easily available, methods use structural information to predict the quality for each residue: Errat (Colovos and Yeates 1993), ProsaII (Sippl 1993), and Verify3D (Lüthy et al. 1992; Eisenberg et al. 1997).”
Using multiple templates to improve quality of homology models in automated homology modeling (2008, unknown): “…models, many methods have been developed to attempt to identify the best model out of a set of predictions (Colovos and Yeates 1993; Sippl 1993; Eisenberg et al. 1997; Wallner and Elofsson 2003), and it has clearly been shown in the latest CASP experiments that consensus methods (Lundstro¨m et…”