kinemage web site

MolProbity web site

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MolProbity Tutorial :: 2013

Using All-Atom Contact Analysis for Model Diagnosis & Repair

Parts

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

Crystallographers can also get MolProbity-style validation in the Phenix crystallographic software system. Rebuilding with all-atom contact analysis and rotamer selection in Coot improves refinement in Phenix.

More Info about validation, all-atom contact analysis, backrubs, etc :

 (1.5MB)
2011Read_VTF_Struct19

• Report of the wwPDB X-ray Validation Task Force:
Read, Adams, Arendall, Brunger, Emsley, et al. (2011) "A New Generation of Crystallographic Validation Tools for the Protein Data Bank" Structure 19: 1395-1412.

 (1.6MB)
2010Chen_molProb_ActaD66

• Latest MolProbity reference:
Chen, Arendall, Headd, Keedy, Immormino, et al. (2010) "MolProbity: all-atom structure validation for macromolecular crystallography" Acta Cryst D66:12-21.

 (0.5MB)
2006DavisStr14

• Backrubs:
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, et al. (2005) "A test of enhancing model accuracy in high-throughput crystallography." Struct Funct Genomics 6:1-11.

 (0.8MB)
2003LovellPsfg50

Lovell, Davis, Arendall, de Bakker, Word, et al. (2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ 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

• H addition and Asn/Gln/His flips:
Word, Lovell, Richardson, & Richardson (1999) "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation." JMB 285: 1735-47.


download arrow 1bkrFH-multi.kin.gz(0.6MB) download arrow 1bkrFH.pdb(0.3MB) download arrow 1BKR.omap.gz(2.5MB)
http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/
Dave & Jane Richardson