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
 (2.5MB)
2013Richardson_CurrOpin
Richardson JS, Prisant MG, Richardson DC (2013) "Crystallographic Model Validation: from Diagnosis to Healing", Curr Opin Struct Biol 23: 707-714​
 (0.75MB)
2012Echols_JAppCryst
Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkoczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD (2012) "Graphical tools for macromolecular crystallography in Phenix", J Applied Crystallogr 45:581-586
 (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.
 (1.6MB)
2010Chen_molProb_ActaD66
Chen, Arendall, Headd, Keedy, Immormino, Kapral, Murray, Richardson, & Richardson (2010) "MolProbity: all-atom structure validation for macromolecular crystallography" Acta Cryst D66:12-21.
 (0.5MB)
2006DavisStr14
Davis, Arendall, Richardson, & Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274.
 (0.8MB)
2003LovellPsfg50
Lovell, Davis, Arendall, de Bakker, Word, Prisant, Richardson, & Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Deviation." Proteins: Struct Funct Genetics 50: 437-450.
 (0.3MB)
2000LovellPsfg40
Lovell, Word, Richardson, & Richardson (2000) "The Penultimate Rotamer Library." Proteins: Struct Funct Genetics 40: 389-408.
 (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/CSHL2016/
Jane & Dave Richardson, & Bradley Hintze