AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR

By Roman A. Laskowski, J.AntoonC. Rullmann, M. MacArthur, R. Kaptein, Janet M. Thornton. 1996

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SHIFTX2: significantly improved protein chemical shift prediction (2011, background): “This is because it is widely acknowledged that most NMR structures do not achieve the coordinate accuracy or precision of high quality X-ray structures (Andrec et al. 2007; Berjanskii et al. 2010; Laskowski et al. 1996; Shen and Bax 2007).”
Assessment of the protein-structure refinement category in CASP8 (2009, methodology): “33–35 For non-stereospecifically assigned hydrogen groups such as methyl and methylene in experiment, pseudo atoms were constructed by AQUA based on geometry average of corresponding proton positions.”
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.”
PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination (2014, methodology): “MolProbity (Chen et al. 2010) and PROCHECK (Laskowski et al. 1996) are also available for structure validation.”
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data (2016, result): “Ramachandran plot analysis results from both Procheck (Laskowski et al. 1996) and MolProbity (Chen et al. 2015) were satisfactory (Supplementary Table S4).”
Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study (2020, unknown): “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.”
RPF: a quality assessment tool for protein NMR structures (2012, methodology): “The five knowledgebased structure quality scores assessed included PROCHECK- /c score (11), the PROCHECK-All dihedral score (11), the Molprobity clash score (12), the Verify3D fold score (9) and the ProsaII fold score (10).”
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models (2017, unknown): “The model quality assessment field has its roots in early structure validation tools (1–3).”