Structure validation: Difference between revisions

Revision as of 07:15, 13 March 2020

Revision as of 14:29, 13 April 2020

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==Historical summary==

Macromolecular crystallography was preceded by the older field of small-molecule [[x-ray crystallography]] (for structures with less than a few hundred atoms). Small-molecule [[diffraction]] data extends to much higher [[Resolution (electron density)|resolution]] than feasible for macromolecules, and has a very clean mathematical relationship between the data and the atomic model. The residual, or R-factor, measures the agreement between the experimental data and the values back-calculated from the atomic model. For a well-determined small-molecule structure the R-factor is nearly as small as the uncertainty in the experimental data (well under 5%). Therefore, that one test by itself provides most of the validation needed, but a number of additional consistency and methodology checks are done by automated software<ref>{{Cite journal | vauthors = Spek AL |year=2003 |title=Single-crystal structure validation with the program PLATON |journal=Journal of Applied Crystallography |volume= 36 |pages=7–13 |doi=10.1107/S0021889802022112|doi-access=free }}</ref> as a requirement for small-molecule crystal structure papers submitted to the [[International Union of Crystallography]] (IUCr) journals such as [[Acta Crystallographica]] section B or C. Atomic coordinates of these small-molecule structures are archived and accessed through the [[Cambridge Structural Database]] (CSD)<ref>{{cite journal | vauthors = Allen FH | title = The Cambridge Structural Database: a quarter of a million crystal structures and rising | journal = Acta Crystallographica Section B | volume = 58 | issue = Pt 3 Pt 1 | pages = 380–8 | date = June 2002 | pmid = 12037359 | doi = 10.1107/S0108768102003890 | doi-access = free }}</ref> or the [[Crystallography Open Database]] (COD).<ref>{{cite journal | vauthors = Gražulis S, Chateigner D, Downs RT, Yokochi AF, Quirós M, Lutterotti L, Manakova E, Butkus J, Moeck P, Le Bail A | display-authors = 6 | title = Crystallography Open Database - an open-access collection of crystal structures | journal = Journal of Applied Crystallography | volume = 42 | issue = Pt 4 | pages = 726–729 | date = August 2009 | pmid = 22477773 | pmc = 3253730 | doi = 10.1107/s0021889809016690 }}</ref>

The first macromolecular validation software was developed around 1990, for proteins. It included Rfree [[cross-validation (statistics)|cross-validation]] for model-to-data match,<ref name="Rfree">{{cite journal | vauthors = Brünger AT | title = Free R value: a novel statistical quantity for assessing the accuracy of crystal structures | journal = Nature | volume = 355 | issue = 6359 | pages = 472–5 | date = January 1992 | pmid = 18481394 | doi = 10.1038/355472a0 | author-link = Axel T. Brunger | bibcode = 1992Natur.355..472B }}</ref> bond length and angle parameters for covalent geometry,<ref name="Engh">{{cite journal |vauthors=Engh RA, Huber R |year=1991 |title=Accurate bond and angle parameters for X-ray protein structure refinement |journal=Acta Crystallographica A |volume=47 |issue=4 |pages=392&ndash;400|doi=10.1107/s0108767391001071 }}</ref> and sidechain and backbone conformational criteria.<ref name="Ponder&Richards">{{cite journal |vauthors=Ponder JW, Richards FM |year=1987 |title=Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes |journal=Journal of Molecular Biology |volume=193 |issue=4 |pages=775–791 |doi=10.1016/0022-2836(87)90358-5|pmid=2441069 }}</ref><ref name="procheck">{{cite journal |vauthors=Laskowski RA, MacArthur MW, Moss DS, Thornton JM |author4-link=Janet Thornton |year=1993 |title=PROCHECK: a program to check the stereochemical quality of protein structures |journal=Journal of Applied Crystallography |volume=26 |issue=2 |pages=283–291 |doi=10.1107/s0021889892009944}}</ref><ref name="whatif">{{cite journal | vauthors = Hooft RW, Vriend G, Sander C, Abola EE | title = Errors in protein structures | journal = Nature | volume = 381 | issue = 6580 | pages = 272 | date = May 1996 | pmid = 8692262 | doi = 10.1038/381272a0 | bibcode = 1996Natur.381..272H }}</ref> For macromolecular structures, the atomic models are deposited in the [[Protein Data Bank]] (PDB), still the single archive of this data. The PDB was established in the 1970s at [[Brookhaven National Laboratory]],<ref>{{cite journal | vauthors = Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M | display-authors = 6 | title = The Protein Data Bank: a computer-based archival file for macromolecular structures | journal = Journal of Molecular Biology | volume = 112 | issue = 3 | pages = 535–42 | date = May 1977 | pmid = 875032 | doi = 10.1016/s0022-2836(77)80200-3 | author7-link = Olga Kennard }}</ref> moved in 2000 to the [http://www.rcsb.org/pdb RCSB] (Research Collaboration for Structural Biology) centered at [[Rutgers]],<ref>{{cite journal | vauthors = Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE | display-authors = 6 | title = The Protein Data Bank | journal = Nucleic Acids Research | volume = 28 | issue = 1 | pages = 235–42 | date = January 2000 | pmid = 10592235 | pmc = 102472 | doi = 10.1093/nar/28.1.235 | author8-link = Philip Bourne | author-link = Helen M. Berman }}</ref> and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank),<ref name="wwPDB">{{cite journal | vauthors = Berman H, Henrick K, Nakamura H | title = Announcing the worldwide Protein Data Bank | journal = Nature Structural Biology | volume = 10 | issue = 12 | pages = 980 | date = December 2003 | pmid = 14634627 | doi = 10.1038/nsb1203-980 | author-link = Helen M. Berman }}</ref> with access sites added in Europe ([http://pdbe.org|PDBe]) and Asia ([http://www.pdbj.org|PDBj]), and with NMR data handled at the [http://www.bmrb.wisc.edu BioMagResBank (BMRB)] in Wisconsin.

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== In SAXS ==

SAXS (small-angle x-ray scattering) is a rapidly growing area of structure determination, both as a source of approximate 3D structure for initial or difficult cases and as a component of hybrid-method structure determination when combined with NMR, EM, crystallographic, cross-linking, or computational information. There is great interest in the development of reliable validation standards for SAXS data interpretation and for quality of the resulting models, but there are as yet no established methods in general use. Three recent steps in this direction are the creation of a Small-Angle Scattering Validation Task Force committee by the worldwide Protein DataBank and its initial report,<ref name="sasVTF">{{cite journal | vauthors = Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM | display-authors = 6 | title = Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB | journal = Structure | volume = 21 | issue = 6 | pages = 875–81 | date = June 2013 | pmid = 23747111 | doi = 10.1016/j.str.2013.04.020 | doi-access = free }}</ref> a set of suggested standards for data inclusion in publications,<ref name="Jacques2012">{{cite journal | vauthors = Jacques DA, Guss JM, Svergun DI, Trewhella J | title = Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution | journal = Acta Crystallographica Section D | volume = 68 | issue = Pt 6 | pages = 620–6 | date = June 2012 | pmid = 22683784 | doi = 10.1107/S0907444912012073 | doi-access = free }}</ref> and an initial proposal of statistically derived criteria for automated quality evaluation.<ref name="Grant2015">{{cite journal | vauthors = Grant TD, Luft JR, Carter LG, Matsui T, Weiss TM, Martel A, Snell EH | title = The accurate assessment of small-angle X-ray scattering data | journal = Acta Crystallographica Section D | volume = 71 | issue = Pt 1 | pages = 45–56 | date = January 2015 | pmid = 25615859 | pmc = 4304685 | doi = 10.1107/S1399004714010876 }}</ref>

==For computational biology==

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**[http://www.saha.ac.in/biop/bioinformatics.html RNAhelix] (RNA validation)

* X-ray

** [http://eds.bmc.uu.se/eds/ EDS (Electron Density Server)]<ref>{{cite journal | vauthors = Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA | title = The Uppsala Electron-Density Server | journal = Acta Crystallographica Section D | volume = 60 | issue = Pt 12 Pt 1 | pages = 2240–9 | date = December 2004 | pmid = 15572777 | doi = 10.1107/s0907444904013253 | doi-access = free }}</ref>

** [[Coot (software)|Coot]] - modeling software (built-in validation) [http://www.biop.ox.ac.uk/coot/]<ref>{{cite journal | vauthors = Emsley P, Lohkamp B, Scott WG, Cowtan K | title = Features and development of Coot | journal = Acta Crystallographica Section D | volume = 66 | issue = Pt 4 | pages = 486–501 | date = April 2010 | pmid = 20383002 | pmc = 2852313 | doi = 10.1107/s0907444910007493 }}</ref>

** [https://pdb-redo.eu/ PDB-REDO] - X-ray model optimization: rebuilding and refining all models using contemporary techniques<ref>{{cite journal | vauthors = Joosten RP, Joosten K, Murshudov GN, Perrakis A | title = PDB_REDO: constructive validation, more than just looking for errors | journal = Acta Crystallographica Section D | volume = 68 | issue = Pt 4 | pages = 484–96 | date = April 2012 | pmid = 22505269 | pmc = 3322608 | doi = 10.1107/s0907444911054515 }}</ref>