MolProbity: More and better reference data for improved all‐atom structure validation

Abstract

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include Additional Supporting Information may be found in the online version of this article.Grant sponsor: National Institutes of health; Grant numbers: R01-GM073919 to DCR, P01-GM063210 subcontract to JSR, R01-GM088674 to JSR, R01-GM073930 to DCR and its ARRA supplement, and DUMC bridge funding. messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Ca-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

“…(SAVES, 2020, Williams et al , 2018). Various types of software were used to judge the validity of the model, such as PROCHECK (Laskowski et al , 1996), Verify 3D (Eisenberg et al , 1997), PROVE (Joan Pontius, 1996), and ERRAT (Hooft et al , 1996), in addition to the Ramachandran plot of the MolProbity web server.…”

Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

“…6NUR, chain A, is a SARS HCoV non-structural protein 12 (nsp12) solved experimentally using cryo-Electron Microscopy (cryo-EM) with 3.1 Å resolution deposited in the protein data bank last year [35]. The Molprobity web server of the Duke University, and the structure analysis and verification server (SAVES) of the University of California Los Angles (UCLA) are used to test the model [36,37]. 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 human coronavirus HCoV-229E S-protein structure and receptor binding

“…The other half-map was used for generating model statistics. The atomic model was validated using Molprobity (Williams et al, 2018), EMRinger (Barad et al, 2015) and the comprehensive validation (cryo-EM) tool in Phenix (Afonine et al, 2018b). The molecular graphics, animations and movies were generated using UCSF Chimera (Pettersen et al, 2004) and UCSF ChimeraX (Goddard et al, 2018).…”