Table 3.
Component Software Packages Included in the 2017 Version of the Validation Pipeline
| Software Package | Which Section and Metric of the Report the Package Is Used for | Reference |
|---|---|---|
| MolProbity | model geometry: bond lengths and bond angles of standard protein residues and nucleotides, too-close contacts, Ramachandran outliers, rotamer outliers, RNA suiteness | Chen et al., 2010 |
| MAXIT | model geometry: symmetry-related too-close contacts, stereochemistry issues, identification of cis-peptides | Maxit (Z.F., https://sw-tools.rcsb.org/apps/MAXIT/index.html) |
| Mogul | model geometry: bond-length and bond-angle outliers in small molecules | Bruno et al., 2004 |
| Xtriage (Phenix) | crystallographic data and refinement statistics: signal-to-noise, twinning | Adams et al., 2010 |
| DCC | crystallographic data and refinement statistics: R, Rfree fit to crystallographic data: Rfree |
Yang et al., 2016 |
| EDS | fit to crystallographic data: real-space R outliers | Kleywegt et al., 2004 |
| Cyrange | NMR ensemble composition: identification of well-defined protein cores | Kirchner and Güntert, 2011 |
| RCI | NMR chemical shifts: prediction of protein backbone order parameter from chemical shifts | Berjanskii and Wishart, 2005 |
| PANAV | NMR chemical shifts: suggested referencing corrections in chemical shift assignments | Wang et al., 2010 |