kinemage web site

MolProbity web site

part 1

part 2

part 3

multi-crit kinemage

1. MolProbity Analysis; Finding Model Anomalies...

Add H, calculate contacts, and assess geometry by running the MolProbity web service

backrub for main chain

2. Rebuilding in KiNG; easy-to-learn alternate correction method,

with explicit Local backbone adjustments, real-time rotamer and contact analysis (but not Coot's crystallographic capabilities).

rotamers & contact dots in O

3. MolProbity-style Validation in PHENIX and Coot

The PHENIX GUI has been linked to COOT allowing interactivity between the GUI and where structure correction can be made. Setup in Phenix GUI: click 'New project', then select 'Set up tutorial data...'

More Info about All-atom Contact Analysis
 (6.9MB)
2017Williams-MolProbity4
Williams, Headd, Moriarty, Prisant1, Videau, Deis, Verma, Keedy, Hintze, Chen, Jain, Lewis, Arendall, Snoeyink, Adams, Lovell, Richardson, & Richardson (2017) "MolProbity: More and better reference data for improved all-atom structure validation" Protein Science (in Press)
 (3.4MB)
2017Richardson
Richardson, Williams, Hintze, Chen, Prisant, Videau, Richardson (2017) "Model validation: local diagnosis, correction and when to quit" Acta Cryst (2017) (in Press)
 (0.6MB)
2016Hintze
Hintze, Lewis, Richardson, & Richardson (2016) "MolProbity's ultimate rotamer-library distributions for model validation" Proteins: Struc Func Bioinf 84: 1177-1189.
 (1.5MB)
2011Read_VTF_Struct19
Read, Adams, Arendall, Brunger, Emsley, Joosten, Kleywegt, Krissinel, Lütteke, Otwinowski, Perrakis, Richardson, Sheffler, Smith, Tickle, Vriend, & Zwart (2011) "A New Generation of Crystallographic Validation Tools for the Protein Data Bank" Structure 19: 1395-1412.
 (0.5MB)
2006DavisStr14
Davis, Arendall, Richardson, & Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274.
 (804KB)
1999WordB
Word, Lovell, Richardson, & Richardson (1999) "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation." J Mol Biol 285: 1735-47.
http://kinemage.biochem.duke.edu/teaching/workshops/CSHL2017/
Jane & Dave Richardson, & Christopher Williams
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