Structure validation

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 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{{Cite journal | vauthors = Spek AL |year=2003 |title=Single-crystal structure validation with the program PLATON |journal=Journal of Applied Crystallography |volume= 36 |issue=1 |pages=7–13 |doi=10.1107/S0021889802022112|bibcode=2003JApCr..36....7S |doi-access=free }} 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){{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 | bibcode = 2002AcCrB..58..380A | doi-access = }} or the Crystallography Open Database (COD).{{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 | bibcode = 2009JApCr..42..726G }}

The first macromolecular validation software was developed around 1990, for proteins. It included Rfree cross-validation for model-to-data match,{{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 | s2cid = 2462215 }} bond length and angle parameters for covalent geometry,{{cite journal |vauthors=Engh RA, Huber R |year=1991 |title=Accurate bond and angle parameters for X-ray protein structure refinement |journal=Acta Crystallographica Section A |volume=47 |issue=4 |pages=392–400|doi=10.1107/s0108767391001071 |bibcode=1991AcCrA..47..392E }} and sidechain and backbone conformational criteria.{{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 }}{{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|bibcode=1993JApCr..26..283L }}{{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 | s2cid = 4368507 | doi-access = free }} 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,{{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 }} moved in 2000 to the [http://www.rcsb.org/pdb RCSB] {{Webarchive|url=https://web.archive.org/web/20080828002005/http://www.rcsb.org./pdb |date=2008-08-28 }} (Research Collaboration for Structural Biology) centered at Rutgers,{{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 }} and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank),{{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 | s2cid = 2616817 | author-link = Helen M. Berman | doi-access = free }} 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.

Validation rapidly became standard in the field,{{cite journal | vauthors = Kleywegt GJ |year= 2000 |title= Validation of protein crystal structures |journal=Acta Crystallographica Section D |volume=56 |issue= Pt 3 |pages=18–19|doi= 10.1107/s0907444999016364 |pmid= 10713511 |bibcode= 2000AcCrD..56..249K }} with further developments described below. *Obviously needs expansion*

A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide Protein Data Bank (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for [http://www.wwpdb.org/validation.html wwPDB deposition] from recommendations of the wwPDB Validation Task Force committees for x-ray crystallography,{{cite journal | vauthors = Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH | display-authors = 6 | title = A new generation of crystallographic validation tools for the protein data bank | journal = Structure | volume = 19 | issue = 10 | pages = 1395–412 | date = October 2011 | pmid = 22000512 | pmc = 3195755 | doi = 10.1016/j.str.2011.08.006 | author12-link = Jane Richardson (chemist) | author7-link = Gerard Kleywegt | author4-link = Axel Brunger }} for NMR,{{cite journal | vauthors = Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL | display-authors = 6 | title = Recommendations of the wwPDB NMR Validation Task Force | journal = Structure | volume = 21 | issue = 9 | pages = 1563–70 | date = September 2013 | pmid = 24010715 | pmc = 3884077 | doi = 10.1016/j.str.2013.07.021 | author12-link = Gerard Kleywegt | author11-link = Helen M. Berman | author3-link = Ad Bax | author6-link = Jane Richardson (chemist) }} for SAXS (small-angle x-ray scattering), and for cryoEM (cryo-Electron Microscopy).{{cite journal | vauthors = Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL | display-authors = 6 | title = Outcome of the first electron microscopy validation task force meeting | journal = Structure | volume = 20 | issue = 2 | pages = 205–14 | date = February 2012 | pmid = 22325770 | pmc = 3328769 | doi = 10.1016/j.str.2011.12.014 | author16-link = Michael Rossmann | author-link = Richard Henderson (biologist) }}

Validations can be broken into three stages: validating the raw data collected (data validation), the interpretation of the data into the atomic model (model-to-data validation), and finally validation on the model itself. While the first two steps are specific to the technique used, validating the arrangement of atoms in the final model is not.

{{cite journal |vauthors=Gelbin A, Schneider B, Clowney L, ((Hsieh S-H)), Olson WK, Berman HM |author6-link=Helen M. Berman |year=1996 |title=Geometric parameters in Nucleic Acids:Sugar and Phosphate Constituents |journal=Journal of the American Chemical Society |volume=118 |issue=3 |pages=519–529 |doi=10.1021/ja9528846}}{{cite journal | vauthors = Schultze P, Feigon J | title = Chirality errors in nucleic acid structures | journal = Nature | volume = 387 | issue = 6634 | pages = 668 | date = June 1997 | pmid = 9192890 | doi = 10.1038/42632 | bibcode = 1997Natur.387..668S | s2cid = 4318780 | doi-access = free }}

The backbone and side-chain dihedral angles of protein and RNA have been shown to have specific combinations of angles which are allowed (or forbidden). For protein backbone dihedrals (φ, ψ), this has been addressed by the legendary Ramachandran Plot while for side-chain dihedrals (χ's), one should refer to the Dunbrack Backbone-dependent rotamer library.{{cite web |title=Smooth Backbone-Dependent Rotamer Library 2010 |url=http://dunbrack.fccc.edu/lab/bbdep2010 |website=dunbrack.fccc.edu |access-date=7 April 2023}}

Though, mRNA structures are generally short-lived and single-stranded, there are an abundance of non-coding RNAs with different secondary and tertiary folding (tRNA, rRNA etc.) which contain a preponderance of the canonical Watson-Crick (WC) base-pairs, together with significant number of non-Watson Crick (NWC) base-pairs - for which such RNA also qualify for regular structural validation that apply for nucleic acid helices. The standard practice is to analyse the intra- (Transnational: Shift, Slide, Rise; Rotational: Tilt, Roll, Twist) and inter-base-pair geometrical parameters (Transnational: Shear, Stagger, Stretch, Rotational: Buckle, Propeller, Opening) - whether in-range or out-of-range with respect to their suggested values.{{Cite journal|last=Dickerson|first=Richard E.|date=1989-02-01|title=Definitions and Nomenclature of Nucleic Acid Structure Parameters|journal=Journal of Biomolecular Structure and Dynamics|volume=6|issue=4|pages=627–634|doi=10.1080/07391102.1989.10507726|issn=0739-1102|pmid=2619931|pmc=400765}}{{Cite journal|last1=Olson|first1=Wilma K|last2=Bansal|first2=Manju|last3=Burley|first3=Stephen K|last4=Dickerson|first4=Richard E|last5=Gerstein|first5=Mark|last6=Harvey|first6=Stephen C|last7=Heinemann|first7=Udo|last8=Lu|first8=Xiang-Jun|last9=Neidle|first9=Stephen|last10=Shakked|first10=Zippora|last11=Sklenar|first11=Heinz|date=2001-10-12|title=A standard reference frame for the description of nucleic acid base-pair geometry11Edited by P. E. Wright22This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.|journal=Journal of Molecular Biology|language=en|volume=313|issue=1|pages=229–237|doi=10.1006/jmbi.2001.4987|issn=0022-2836|pmid=11601858}} These parameters describe the relative orientations of the two paired bases with respect to each other in two strands (intra) along with those of the two stacked base pairs (inter) with respect to each other, and, hence, together, they serve to validate nucleic acid structures in general. Since, RNA-helices are small in length (average: 10-20 bps), the use of electrostatic surface potential as a validation parameter {{Cite journal|last1=Bhattacharyya|first1=Dhananjay|last2=Halder|first2=Sukanya|last3=Basu|first3=Sankar|author3-link=Sankar Basu|last4=Mukherjee|first4=Debasish|last5=Kumar|first5=Prasun|last6=Bansal|first6=Manju|date=2017-01-19|title=RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs|journal=Journal of Computer-Aided Molecular Design|volume=31|issue=2|pages=219–235|doi=10.1007/s10822-016-0007-0|pmid=28102461|bibcode=2017JCAMD..31..219B|s2cid=356097|issn=0920-654X}} has been found to be beneficial, particularly for modelling purposes.

For globular proteins, interior atomic packing (arising from short-range, local interactions) of side-chains{{Cite journal| vauthors = Shen MY, Davis FP, Sali A |date= March 2005|title=The optimal size of a globular protein domain: A simple sphere-packing model|journal=Chemical Physics Letters|volume=405|issue=1–3|pages=224–228|doi=10.1016/j.cplett.2005.02.029|issn=0009-2614|bibcode= 2005CPL...405..224S}}{{cite journal | vauthors = Misura KM, Morozov AV, Baker D | title = Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction | journal = Journal of Molecular Biology | volume = 342 | issue = 2 | pages = 651–64 | date = September 2004 | pmid = 15327962 | doi = 10.1016/j.jmb.2004.07.038 }}{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs | journal = BMC Bioinformatics | volume = 12 | issue = 1 | pages = 195 | date = May 2011 | pmid = 21605466 | pmc = 3123238 | doi = 10.1186/1471-2105-12-195 | doi-access = free }}{{cite journal | vauthors = Banerjee R, Sen M, Bhattacharya D, Saha P | title = The jigsaw puzzle model: search for conformational specificity in protein interiors | journal = Journal of Molecular Biology | volume = 333 | issue = 1 | pages = 211–26 | date = October 2003 | pmid = 14516754 | doi = 10.1016/j.jmb.2003.08.013 }} has been shown to be pivotal in the structural stabilization of the protein-fold. On the other hand, the electrostatic harmony (non-local, long-range) of the overall fold{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Self-complementarity within proteins: bridging the gap between binding and folding | journal = Biophysical Journal | volume = 102 | issue = 11 | pages = 2605–14 | date = June 2012 | pmid = 22713576 | pmc = 3368132 | doi = 10.1016/j.bpj.2012.04.029 | bibcode = 2012BpJ...102.2605B }} has also been shown to be essential for its stabilization. Packing anomalies include steric clashes,{{cite journal | vauthors = Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC | display-authors = 6 | title = MolProbity: all-atom structure validation for macromolecular crystallography | journal = Acta Crystallographica Section D | volume = 66 | issue = Pt 1 | pages = 12–21 | date = January 2010 | pmid = 20057044 | pmc = 2803126 | doi = 10.1107/S0907444909042073 | bibcode = 2010AcCrD..66...12C }} short contacts, holes{{cite journal | vauthors = Sheffler W, Baker D | title = RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation | journal = Protein Science | volume = 18 | issue = 1 | pages = 229–39 | date = January 2009 | pmid = 19177366 | pmc = 2708028 | doi = 10.1002/pro.8 }} and cavities{{cite journal | vauthors = Chakravarty S, Varadarajan R | title = Residue depth: a novel parameter for the analysis of protein structure and stability | journal = Structure | volume = 7 | issue = 7 | pages = 723–32 | date = July 1999 | pmid = 10425675 | doi = 10.1016/s0969-2126(99)80097-5 | doi-access = free }} while electrostatic disharmony{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Applications of complementarity plot in error detection and structure validation of proteins | journal = Indian Journal of Biochemistry & Biophysics | volume = 51 | issue = 3 | pages = 188–200 | date = June 2014 | pmid = 25204080 }} refer to unbalanced partial charges in the protein core (particularly relevant for designed protein interiors). While the clash-score of [http://molprobity.biochem.duke.edu/ Molprobity] identifies steric clashes at a very high resolution, the Complementarity Plot combines packing anomalies with electrostatic imbalance of side-chains and signals for either or both.

File:(A)-ASN297.svg

The branched and cyclic nature of carbohydrates poses particular problems to structure validation tools.{{cite journal | vauthors = Agirre J, Davies GJ, Wilson KS, Cowtan KD | title = Carbohydrate structure: the rocky road to automation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 39–47 | date = June 2017 | pmid = 27940408 | doi = 10.1016/j.sbi.2016.11.011 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf | series = Carbohydrates • Sequences and topology }} At higher resolutions, it is possible to determine the sequence/structure of oligo- and poly-saccharides, both as covalent modifications and as ligands. However, at lower resolutions (typically lower than 2.0Å), sequences/structures should either match known structures, or be supported by complementary techniques such as Mass Spectrometry.{{cite journal | vauthors = Crispin M, Stuart DI, Jones EY | title = Building meaningful models of glycoproteins | journal = Nature Structural & Molecular Biology | volume = 14 | issue = 5 | pages = 354; discussion 354–5 | date = May 2007 | pmid = 17473875 | doi = 10.1038/nsmb0507-354a | s2cid = 2020697 | doi-access = free }} Also, monosaccharides have clear conformational preferences (saturated rings are typically found in chair conformations),{{cite journal | vauthors = Davies GJ, Planas A, Rovira C | title = Conformational analyses of the reaction coordinate of glycosidases | journal = Accounts of Chemical Research | volume = 45 | issue = 2 | pages = 308–16 | date = February 2012 | pmid = 21923088 | doi = 10.1021/ar2001765 }} but errors introduced during model building and/or refinement (wrong linkage chirality or distance, or wrong choice of model - see{{cite journal | vauthors = Agirre J | title = Strategies for carbohydrate model building, refinement and validation | journal = Acta Crystallographica Section D | volume = 73 | issue = Pt 2 | pages = 171–186 | date = February 2017 | pmid = 28177313 | pmc = 5297920 | doi = 10.1107/S2059798316016910 | bibcode = 2017AcCrD..73..171A | url = http://journals.iucr.org/d/issues/2017/02/00/ba5257/ }} for recommendations on carbohydrate model building and refinement and{{cite journal | vauthors = Lütteke T | title = Analysis and validation of carbohydrate three-dimensional structures | journal = Acta Crystallographica Section D | volume = 65 | issue = Pt 2 | pages = 156–68 | date = February 2009 | pmid = 19171971 | pmc = 2631634 | doi = 10.1107/S0907444909001905 | bibcode = 2009AcCrD..65..156L }}{{cite book | vauthors = Lütteke T, von der Lieth CW | title = Glycomics | chapter = Data mining the PDB for glyco-related data | series = Methods in Molecular Biology | volume = 534 | pages = 293–310 | date = 2009-01-01 | pmid = 19277543 | doi = 10.1007/978-1-59745-022-5_21 | isbn = 978-1-58829-774-7 }}{{cite journal | vauthors = Joosten RP, Lütteke T | title = Carbohydrate 3D structure validation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 9–17 | date = June 2017 | pmid = 27816840 | doi = 10.1016/j.sbi.2016.10.010 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf }} for reviews on general errors in carbohydrate structures) can bring their atomic models out of the more likely low-energy state. Around 20% of the deposited carbohydrate structures are in a higher-energy conformation not justified by the structural data (measured using real-space correlation coefficient).{{cite journal | vauthors = Agirre J, Davies G, Wilson K, Cowtan K | title = Carbohydrate anomalies in the PDB | journal = Nature Chemical Biology | volume = 11 | issue = 5 | pages = 303 | date = May 2015 | pmid = 25885951 | doi = 10.1038/nchembio.1798 | url = http://eprints.whiterose.ac.uk/95242/1/AgirreDaviesWIlsonCowtan_self_archived.pdf | doi-access = free }}

A number of carbohydrate validation web services are available at [http://ww.glycosciences.de glycosciences.de] (including nomenclature checks and linkage checks by [http://www.glycosciences.de/tools/pdb-care/ pdb-care],{{cite journal | vauthors = Lütteke T, von der Lieth CW | title = pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files | journal = BMC Bioinformatics | volume = 5 | pages = 69 | date = June 2004 | pmid = 15180909 | pmc = 441419 | doi = 10.1186/1471-2105-5-69 | doi-access = free }} and cross-validation with Mass Spectrometry data through the use of GlycanBuilder), whereas the CCP4 suite currently distributes [http://www.ccp4.ac.uk/html/privateer.html Privateer],{{cite journal | vauthors = Agirre J, Iglesias-Fernández J, Rovira C, Davies GJ, Wilson KS, Cowtan KD | title = Privateer: software for the conformational validation of carbohydrate structures | journal = Nature Structural & Molecular Biology | volume = 22 | issue = 11 | pages = 833–4 | date = November 2015 | pmid = 26581513 | doi = 10.1038/nsmb.3115 | s2cid = 33800088 | url = http://eprints.whiterose.ac.uk/95794/1/Privateer_selfarchived.pdf }} which is a tool that is integrated into the model building and refinement process itself. Privateer is able to check stereo- and regio-chemistry, ring conformation and puckering, linkage torsions, and real-space correlation against positive omit density, generating aperiodic torsion restraints on ring bonds, which can be used by any refinement software in order to maintain the monosaccharide's minimal energy conformation.

Privateer also generates scalable two-dimensional SVG diagrams according to the Essentials of Glycobiology{{cite journal | vauthors = Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S | display-authors = 6 | title = Symbol Nomenclature for Graphical Representations of Glycans | journal = Glycobiology | volume = 25 | issue = 12 | pages = 1323–4 | date = December 2015 | pmid = 26543186 | pmc = 4643639 | doi = 10.1093/glycob/cwv091 }} standard symbol nomenclature containing all the validation information as tooltip annotations (see figure). This functionality is currently integrated into other CCP4 programs, such as the molecular graphics program CCP4mg (through the Glycoblocks 3D representation,{{cite journal | vauthors = McNicholas S, Agirre J | title = Glycoblocks: a schematic three-dimensional representation for glycans and their interactions | journal = Acta Crystallographica Section D | volume = 73 | issue = Pt 2 | pages = 187–194 | date = February 2017 | pmid = 28177314 | pmc = 5297921 | doi = 10.1107/S2059798316013553 | bibcode = 2017AcCrD..73..187M }} which conforms to the standard symbol nomenclature) and the suite's graphical interface, CCP4i2.

{{see also|X-ray crystallography}}

Many evaluation criteria apply globally to an entire experimental structure, most notably the resolution, the anisotropy or incompleteness of the data, and the residual or R-factor that measures overall model-to-data match (see below). Those help a user choose the most accurate among related Protein Data Bank entries to answer their questions. Other criteria apply to individual residues or local regions in the 3D structure, such as fit to the local electron density map or steric clashes between atoms. Those are especially valuable to the structural biologist for making improvements to the model, and to the user for evaluating the reliability of that model right around the place they care about - such as a site of enzyme activity or drug binding. Both types of measures are very useful, but although global criteria are easier to state or publish, local criteria make the greatest contribution to scientific accuracy and biological relevance. As expressed in the Rupp textbook, "Only local validation, including assessment of both geometry and electron density, can give an accurate picture of the reliability of the structure model or any hypothesis based on local features of the model."{{harvnb|Rupp|2009|loc=Chapter 13, Key Concepts}}

Image:Low vs high resolution hemoglobin detail.jpg

;AVS: Assignment validation suite ([https://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for problems.{{cite journal | vauthors = Moseley HN, Sahota G, Montelione GT | title = Assignment validation software suite for the evaluation and presentation of protein resonance assignment data | journal = Journal of Biomolecular NMR | volume = 28 | issue = 4 | pages = 341–55 | date = April 2004 | pmid = 14872126 | doi = 10.1023/B:JNMR.0000015420.44364.06 | s2cid = 14483199 }}

;PSVS: Protein Structure Validation Server at the NESG based on information retrieval statistics{{cite journal | vauthors = Huang YJ, Powers R, Montelione GT | title = Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics | journal = Journal of the American Chemical Society | volume = 127 | issue = 6 | pages = 1665–74 | date = February 2005 | pmid = 15701001 | doi = 10.1021/ja047109h }}

;PROSESS: PROSESS (Protein Structure Evaluation Suite & Server) is a new web server that offers an assessment of protein structural models by NMR chemical shifts as well as NOEs, geometrical, and knowledge-based parameters.

;LACS:Linear analysis of chemical shifts is used for absolute referencing of chemical shift data.

TALOS+. Predicts protein backbone torsion angles from chemical shift data. Frequently used to generate further restraints applied to a structure model during refinement.

Image:2k5d NMR ensemble ribbons.jpg

One of the critical needs for NMR structural ensemble validation is to distinguish well-determined regions (those that have experimental data) from regions that are highly mobile and/or have no observed data. There are several current or proposed methods for making this distinction such as Random Coil Index, but so far the NMR community has not standardized on one.

Cyro-EM presents special challenges to model-builders as the observed electron density is frequently insufficient to resolve individual atoms, leading to a higher likelihood of errors.

Geometry-based validation tools similar to those used in X-ray crystallography can be used to highlight implausible modeling choices and guide modeler toward more native-like structures. The CaBLAM method, which only uses Cα atoms,{{cite web |title=CaBLAM Validation in Phenix |url=https://phenix-online.org/documentation/reference/cablam_validation.html |website=phenix-online.org}} is suitable for low-resolution structures from cyro-EM.{{cite journal |last1=Rohou |first1=Alexis |title=Improving cryo-EM structure validation |journal=Nature Methods |date=February 2021 |volume=18 |issue=2 |pages=130–131 |doi=10.1038/s41592-021-01062-1|pmid=33542515 |s2cid=231820981 }}

A way to compute the difference density map has been formulated for cyro-EM.{{cite journal |last1=Yamashita |first1=Keitaro |last2=Palmer |first2=Colin M. |last3=Burnley |first3=Tom |last4=Murshudov |first4=Garib N. |title=Cryo-EM single-particle structure refinement and map calculation using Servalcat |journal=Acta Crystallographica Section D |date=1 October 2021 |volume=77 |issue=10 |pages=1282–1291 |doi=10.1107/S2059798321009475 |pmid=34605431 |pmc=8489229 |bibcode=2021AcCrD..77.1282Y |doi-access=free |quote=}} Cross-validation using a "free" map, comparable to the use of a free R-factor, is also available.{{cite journal |last1=Falkner |first1=B |last2=Schröder |first2=GF |title=Cross-validation in cryo-EM-based structural modeling. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=28 May 2013 |volume=110 |issue=22 |pages=8930–5 |doi=10.1073/pnas.1119041110 |pmid=23674685|pmc=3670386 |bibcode=2013PNAS..110.8930F |doi-access=free }}{{cite journal |last1=Beckers |first1=Maximilian |last2=Mann |first2=Daniel |last3=Sachse |first3=Carsten |title=Structural interpretation of cryo-EM image reconstructions |journal=Progress in Biophysics and Molecular Biology |date=March 2021 |volume=160 |pages=26–36 |doi=10.1016/j.pbiomolbio.2020.07.004 |pmid=32735944 |doi-access=free}} Other methods for checking model-map fit include correlation coefficients, model-map FSC,{{cite web |title=Cryo-EM Validation tools in Phenix |url=https://phenix-online.org/documentation/reference/validation_cryo_em.html |website=phenix-online.org |language=en}} confidence maps, CryoEF (orientation bias check), and TEMPy SMOC.{{cite web |last1=Winn |first1=Martyn |title=Cryo-EM validation tools in CCP-EM |url=https://www.ccpem.ac.uk/training/validation_symposium_2020/Winn_validation_in_CCP-EM_201120.pdf |publisher=www.ccpem.ac.uk/ |access-date=22 November 2023 |date=20 November 2020}}

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,{{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 }} a set of suggested standards for data inclusion in publications,{{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 | bibcode = 2012AcCrD..68..620J | doi-access = free | hdl = 10453/119226 | hdl-access = free }} and an initial proposal of statistically derived criteria for automated quality evaluation.{{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 | bibcode = 2015AcCrD..71...45G }}

It is difficult to do meaningful validation of an individual, purely computational, macromolecular model in the absence of experimental data for that molecule, because the model with the best geometry and conformational score may not be the one closest to the right answer. Therefore, much of the emphasis in validation of computational modeling is in assessment of the methods. To avoid bias and wishful thinking, double-blind prediction competitions have been organized, the original example of which (held every 2 years since 1994) is CASP (Critical Assessment of Structure Prediction) to evaluate predictions of 3D protein structure for newly solved crystallographic or NMR structures held in confidence until the end of the relevant competition.{{cite journal | vauthors = Moult J, Pedersen JT, Judson R, Fidelis K | title = A large-scale experiment to assess protein structure prediction methods | journal = Proteins | volume = 23 | issue = 3 | pages = ii-v | date = November 1995 | pmid = 8710822 | doi = 10.1002/prot.340230303 | s2cid = 11216440 | url = https://zenodo.org/record/1229334 }} The major criterion for CASP evaluation is a weighted score called GDT-TS for the match of Calpha positions between the predicted and the experimental models.{{cite journal | vauthors = Zemla A | title = LGA: A method for finding 3D similarities in protein structures | journal = Nucleic Acids Research | volume = 31 | issue = 13 | pages = 3370–4 | date = July 2003 | pmid = 12824330 | pmc = 168977 | doi = 10.1093/nar/gkg571 }}

• List of biophysically important macromolecular crystal structures

{{Reflist|30em}}

• Computational prediction
• [http://predictioncenter.org/ CASP experiments home page]
• [http://www.yasara.org/validation.htm/ Model validation in Yasara]
• General-purpose structure validation
• [http://validate.rcsb.org/ validation/deposition site] ([https://validate.wwpdb.org wwPDB] version)
• [http://molprobity.biochem.duke.edu/ MolProbity web service] (has NMR-specific features)
• PDBREPORT ([http://swift.cmbi.ru.nl/gv/pdbreport/index.html]) Protein structure validation database
• [http://swift.cmbi.ru.nl/gv/whatcheck/ What_Check software] {{Webarchive|url=https://web.archive.org/web/20110501180954/http://swift.cmbi.ru.nl/gv/whatcheck/ |date=2011-05-01 }}
• [http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ ProCheck software]
• [http://www.saha.ac.in/biop/www/sarama.html Complementarity Plot]
• [http://www.glycosciences.de/tools/pdb-care/ pdb-care (carbohydrate validation)]
• [http://www.ccp4.ac.uk/html/privateer.html Privateer (carbohydrate validation)]
• [http://xray.bmc.uu.se/usf/ OOPS2, part of the Uppsala Software Factory]
• [https://prosa.services.came.sbg.ac.at/prosa.php ProSA web service]
• [http://services.mbi.ucla.edu/Verify_3D/ Verify-3D profile analysis]
• [http://nucleix.mbu.iisc.ernet.in/nuparmplus/ NUPARM] (Nucleic Acid validation)
• [http://www.saha.ac.in/biop/bioinformatics.html RNAhelix] (RNA validation)
• X-ray
• [http://eds.bmc.uu.se/eds/ EDS (Electron Density Server)] {{Webarchive|url=https://web.archive.org/web/20170702033817/http://eds.bmc.uu.se/eds/ |date=2017-07-02 }}{{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 | bibcode = 2004AcCrD..60.2240K | doi-access = free }}
• Coot - modeling software (built-in validation) [http://www.biop.ox.ac.uk/coot/]{{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 | bibcode = 2010AcCrD..66..486E }}
• [https://pdb-redo.eu/ PDB-REDO] - X-ray model optimization: rebuilding and refining all PDB models using up-to-date techniques{{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 | bibcode = 2012AcCrD..68..484J }}
• PROSESS - Protein Structure Evaluation Suite & Server
• Resolution by Proxy, ResProx - protein model resolution-by-proxy
• [http://vadar.wishartlab.com/ VADAR - Volume, Area, Dihedral Angle Reporter]
• NMR
• [http://psvs-1_4-dev.nesg.org/ PSVS (Protein Structure Validation Server at the NESG)]
• [http://code.google.com/p/cing/ CING (Common Interface for NMR structure Generation) software]
• [http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ ProCheck] - stereochemical quality check for X-ray and NMR{{cite journal | vauthors = Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM | title = AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR | journal = Journal of Biomolecular NMR | volume = 8 | issue = 4 | pages = 477–86 | date = December 1996 | pmid = 9008363 | doi = 10.1007/bf00228148 | s2cid = 45664105 }}
• [http://spin.niddk.nih.gov/bax/nmrserver/talos/ TALOS+ Software & Server] (server for predicting protein backbone torsion angles from chemical shift)
• [http://vadar.wishartlab.com/ VADAR - Volume, Area, Dihedral Angle Reporter]
• PROSESS - Protein Structure Evaluation Suite & Server
• [http://resprox.ca/ ResProx - protein model resolution-by-proxy]
• Cyro-EM
• [http://emdatabank.org/deposit.html EM Data Bank, for EM map deposition]
• [http://www.wwpdb.org/em/ EMDB at the PDB, info on ftp download of maps]
• [https://cci.lbl.gov/ceres CERES], rebuilds (and hopefully improves) Cyro-EM models using the latest version of PHENIX{{cite journal |last1=Liebschner |first1=D |last2=Afonine |first2=PV |last3=Moriarty |first3=NW |last4=Poon |first4=BK |last5=Chen |first5=VB |last6=Adams |first6=PD |title=CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. |journal=Acta Crystallographica Section D |date=1 January 2021 |volume=77 |issue=Pt 1 |pages=48–61 |doi=10.1107/S2059798320015879 |pmid=33404525|pmc=7787109 |bibcode=2021AcCrD..77...48L |doi-access=free }}

{{reflist}}

{{Refbegin}}

• {{Cite book | last1 = Cavanagh | first1 = John | last2 = Fairbrother | first2 = Wayne J. | last3 = Palmer | first3 = Arthur G. III | last4 = Skelton | first4 = Nicholas J. | name-list-style = vanc |title=Protein NMR Spectroscopy: Principles and Practice |edition=2nd |year=2006 |publisher=Academic Press |isbn=978-0-12-164491-8 |ref={{harvid|Cavanagh|2006}} }}
• {{Cite book |last= Rupp |first=Bernhard | name-list-style = vanc |title=Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology |year=2009 |publisher=Garland Science |isbn=978-0815340812 }}

{{Refend}}

Category:Structural biology

Category:Protein methods

Category:Protein structure