[CSHL Web Site]

kinemage web site

MolProbity web site

part 1

part 2

part 3

part 4

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

3. All-atom Contact Tools in Coot

Rebuilding with all-atom contact analysis along with rotamer selection in Coot

All-atom contact dots

4. Further exercises

try one or more of these

More Info about All-atom Contact Analysis

 (2.2MB)
2007DavisNAR35

Davis, Leaver-Fay, Chen, Block, Kapral, Wang, Murray, Arendall, Snoeyink, Richardson & Richardson (2007) "MolProbity: all-atom contacts and structure validation for proteins and nucleic acids" Nucleic Acids Research 35(Web Server Issue):W375-383

 (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." 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." JMB 285: 1735-47.

http://kinemage.biochem.duke.edu/teaching/csh/
Jane & Dave Richardson