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

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

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/CSHL2012/
Jane & Dave Richardson, & Jeff Headd