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1. MolProbity AnalysisAdd H, calculate contacts, and assess geometry by running the MolProbity web service |
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2. Rebuilding in KiNGLocal backbone adjustments using KiNG |
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3. MolProbity-style Validation in PHENIX and CootPHENIX has built-in MolProbity tools, and can interactively call Coot, which in turn can show all-atom-contacts |
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4. Further Exercisestry one or more of these |
![]() 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. |
![]() 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. |
![]() 2006DavisStr14 |
Davis, Arendall, Richardson, & Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274. |
![]() 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. |
![]() 2003LovellPsfg50 |
Lovell, Davis, Arendall, de Bakker, Word, Prisant, Richardson, & Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation." Proteins: Struct Funct Genetics 50: 437-450. |
![]() 2000LovellPsfg40 |
Lovell, Word, Richardson, & Richardson (2000) "The Penultimate Rotamer Library." Proteins: Struct Funct Genetics 40: 389-408. |
![]() 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. |