Quality control of protein models : directional atomic contact analysis

By G. Vriend, Christopher Sander. 1993

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. Robbie P. Joosten
2. F. Long
3. Anastassis Perrakis
4. G. Murshudov
5. N. V. Dokholyan
6. Srinivas Ramachandran
7. Feng Ding
8. Pradeep Kota

Citations in the corpus

• Automated Minimization of Steric Clashes in Protein Structures (2011, background): “For instance, WHAT_CHECK5,6 and Molprobity,7 commonly used in protein quality control, report a steric clash based on distances between two atoms with a distance cutoff for overlap set to 0.4 A˚.”
• The PDB_REDO server for macromolecular structure model optimization (2014, methodology): “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”
• Developing optimal non-linear scoring function for protein design (2004, methodology): “Whatif database contains less structures than Pdbselect because the R-factor and resolution criteria are more stringent (Vriend and Sander, 1993).”