X-Ray Methods In Structural Biology -- CSHL

Using All-Atom Contact Analysis for Model Diagnosis & Repair

1. MolProbity Analysis

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

2. Rebuilding in KiNG

Local backbone adjustments using KiNG.

3. All-atom Contact Tools in Coot

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

4. Further exercises

Try one or more of these.

More Info about All-atom Contact Analysis

Hintze, Lewis, Richardson & Richardson. "MolProbity's ultimate rotamer-library distributions for model validation". (2016) Proteins: Struc Func Bioinf 84 online since Mar 28 https://doi.org/10.1002/prot.25039
Williams, Hintze, Headd, Moriarty, Chen, Jain, Prisant, Lewis, Videau, Keedy, Deis, Arendall, Verma, Snoeyink, Adams, Lovell, Richardson & Richardson. "MolProbity: More and better reference data for improved all-atom structure validation". (2018) ProtSci 27 293-315 doi: 10.1002/pro.3330, PMC5734394 https://doi.org/10.1002/pro.3330
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 https://doi.org/10.1093/nar/gkh398
Davis, Arendall, Richardson, & Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274 https://doi.org/10.1016/j.str.2005.10.007
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. https://doi.org/10.1007/s10969-005-3138-4
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. https://doi.org/10.1002/prot.10286
Word, Lovell, Richardson, & Richardson (1999) "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation." JMB 285: 1735-47. https://doi.org/10.1006/jmbi.1998.2401
http://kinemage.biochem.duke.edu/teaching/csh/
Jane & Dave Richardson