kinemage web site

MolProbity web site

part 1

part 2

part 3

part 4

multi-crit kinemage

1. MolProbity Analysis

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

backrub for main chain

2. Rebuilding in KiNG

Local backbone adjustments using KiNG

rotamers & contact dots in O

3. MolProbity-style Validation in PHENIX and Coot

PHENIX has built-in MolProbity tools, and can interactively call Coot, which in turn can show all-atom-contacts

All-atom contact dots

4. Further Exercises

try one or more of these

More Info about All-atom Contact Analysis

 (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.

 (0.4MB)
2005ArendallJFSG6

Arendall, Tempel, Richardson, Zhou, Wang, Davis, Liu, Rose, Carson, Luo, Richardson, & Wang (2005) "A test of enhancing model accuracy in high-throughput crystallography." J Struct Funct Genomics 6: 1-11.

 (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/workshop/MolProbity/
Jane & Dave Richardson