Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

By J. Word, S. Lovell, T. LaBean, Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, David C Richardson. 1999

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Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “, the number of all types of steric clashes per thousand residues.(28) The assessment also considered the coordinate comparison metric TM-score as computed in RNA-Align(29) and the Mean of Circular Quantities(30) to assess accuracy in the torsion angle space.”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “For proteins, the open-source DSSP[57] derived program “ksdssp” is used to identify helices and sheets; for nucleic acids, REDUCE and PROBE[58] are used to identify hydrogen bonds, from which Watson-Crick, G-U base pairs and Saenger base pairs[59] are extracted.”
RNA Structure Refinement using the ERRASER-Phenix pipeline (2013, background): “These include: - Steric clashes (21), defined as atomic overlaps of at least 0.”
MolProbity: More and better reference data for improved all‐atom structure validation (2018, background): “The standard MolProbity all-atom contact representation, 8 both for scoring and for visualization, consists of paired patches of dots (or overlap spikes) on the surface of each atom of the contacting pair.”
Assessment of the protein-structure refinement category in CASP8 (2009, methodology): “20 The MolProbity score21 is calculated as: where C LASH S CORE is the number of unfavorable steric overlaps (cid:2) 0.4 A˚ as calculated by Probe,22 R OTA O UT is the percentage of rotamer conformations classified as outliers and R AMMA I FFY is the percentage of backbone conformations classified a”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, background): “All-atom contacts [ 59 ] contributed a new major source of independent information by adding, optimizing, and analyzing the other half of the atoms — the hydrogens — and analyzing their steric clashes as well as their H-bonding.”
A graph‐theory algorithm for rapid protein side‐chain prediction (2003, unknown): “These include steric checks on hydrogen atoms (Word et al. 1999a) and B-factor cutoffs of 30.”
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools (2019, methodology): “All-atom contacts are computed by PROBE (65) that uses van der Waals atom radii and identifies probes intersecting any not-covalently-bonded atom.”