The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!

NATO Science for Peace and Security Series A: Chemistry and Biology

Volumn , Issue , 2013, Pages 1-10

  Richardson, Jane S ^a   Richardson, David C ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

All atom contacts; Model improvement; Model validation; MolProbity; RNA backbone

Indexed keywords

EID: 84877061186     PISSN: 18746489     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-007-6232-9_1     Document Type: Article

References (33)

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13. Lovell SC, Davis IW, Arendall WB III, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Ca geometry: ¥, § and C" deviation. Proteins: Struct Funct Genetics 50:437-450
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17. Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature. RNA 14:465-481 (open access
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20. Word JM, Lovell SC, LaBean TH, Zalis ME, Presley BK, Richardson JS, Richardson DC (1999) Visualizing and quantitating molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285:1711-1733
21. Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735-1747
22. EDS (Electron Density Server): http://eds.bmc.uu.se/eds
23. MolProbity service: http://molprobity.biochem.duke.edu
24. PDB (at RCSB) Validation Server: http://validate.rcsb.org
25. PDBsum (ProCheck) is linked from the specific PDB page, eg for 1ubq: http://www.ebi.ac.uk/ thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?template= main.html&o=PROCHECK& c=999&pdbcode=1UBQ
26. Phenix: http://phenix-online.org
27. ProSA-web: https://prosa.services.came.sbg.ac.at/prosa.php
28. Richardson Lab for KiNG, Reduce, Suitename, Top8000, etc: http://kinemage.biochem.duke. edu
29. Verify3D profile analysis: http://nihserver.mbi.ucla.edu/Verify 3D
30. WhatCheck: http://swift.cmbi.ru.nl/gv/whatcheck
31. Wikipedia article: https://en.wikipedia.org/wiki/Structure validation
32. wwPDB info about referee validation reports: http://www.wwpdb.org/ validation.html
33. wwPDB link to Xray Validation Task Force: http://www.wwpdb.org/workshop/ 2011