Errors in protein structures

By Rob W. W. Hooft, G. Vriend, Christopher Sander, E. Abola. 1996

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Features and development of Coot (2010, neutral): “The integration of validation tools will be expanded, especially with respect to MolProbity , and an interface to the WHAT_CHECK validation program (Hooft et al. , 1996) will be added.”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, background): “18,27,37 An important question is how the new system will change rotamer analysis, specifically the number and identity of outliers.”
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank (2005, background): “can be related to the NMR data themselves (restraint violations, NOE completeness,(11) information content(12)), to the precision of the ensembles or to several structural features of the coordinate data, often expressed as normality scores relative to an X-ray database.(13,14) Several studies have ”
The PDB_REDO server for macromolecular structure model optimization (2014, background): “Specific amendments to the PDB_REDO pipeline The PDB_REDO procedure consists of model refinement in REFMAC (Murshudov et al., 1997, 2011), rebuilding by Centrifuge (which deletes waters without electron density), SideAide [which (re)builds side chains in rotameric conformations] and pepflip (which f”
Assessment of template based protein structure predictions in CASP9 (2011, methodology): “While the usage of validation tools like WhatIf,23 ProCheck,24 or Molprobity25 is standard procedure in the field of experimental structural biology, stereo-chemically incorrect structure predictions are still encountered rather frequently.”
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.”
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).”
Objectively judging the quality of a protein structure from a Ramachandran plot (1997, methodology): “The Ramachandran plot quality analysis is available as part of the WHAT_CHECK program (Hooft et al., 1996b).”
PISCES: a protein sequence culling server (2003, methodology): “Some missing values are obtained from the PDBFINDER database (Hooft et al., 1996).”
Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection (2006, methodology): “with default settings and accuracy of the RNASEH2A protein (NP_006388) predicted structure validated by WHAT_CHEC”