{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T19:03:18Z","timestamp":1784055798746,"version":"3.55.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,9,18]],"date-time":"2007-09-18T00:00:00Z","timestamp":1190073600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-345","type":"journal-article","created":{"date-parts":[[2007,9,18]],"date-time":"2007-09-18T14:13:22Z","timestamp":1190124802000},"source":"Crossref","is-referenced-by-count":66,"title":["Benchmarking consensus model quality assessment for protein fold recognition"],"prefix":"10.1186","volume":"8","author":[{"given":"Liam J","family":"McGuffin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,9,18]]},"reference":[{"issue":"2","key":"1717_CR1","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.sbi.2006.03.004","volume":"16","author":"D Fischer","year":"2006","unstructured":"Fischer D: Servers for protein structure prediction. Curr Opin Struct Biol 2006, 16(2):178\u2013182. 10.1016\/j.sbi.2006.03.004","journal-title":"Curr Opin Struct Biol"},{"issue":"4","key":"1717_CR2","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1007\/BF00228148","volume":"8","author":"RA Laskowski","year":"1996","unstructured":"Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM: AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996, 8(4):477\u2013486. 10.1007\/BF00228148","journal-title":"J Biomol NMR"},{"issue":"6580","key":"1717_CR3","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/381272a0","volume":"381","author":"RW Hooft","year":"1996","unstructured":"Hooft RW, Vriend G, Sander C, Abola EE: Errors in protein structures. Nature 1996, 381(6580):272. 10.1038\/381272a0","journal-title":"Nature"},{"issue":"2","key":"1717_CR4","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/S0959-440X(00)00063-4","volume":"10","author":"T Lazaridis","year":"2000","unstructured":"Lazaridis T, Karplus M: Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000, 10(2):139\u2013145. 10.1016\/S0959-440X(00)00063-4","journal-title":"Curr Opin Struct Biol"},{"issue":"4","key":"1717_CR5","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1002\/prot.340170404","volume":"17","author":"MJ Sippl","year":"1993","unstructured":"Sippl MJ: Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17(4):355\u2013362. 10.1002\/prot.340170404","journal-title":"Proteins"},{"key":"1717_CR6","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1016\/S0076-6879(97)77022-8","volume":"277","author":"D Eisenberg","year":"1997","unstructured":"Eisenberg D, Luthy R, Bowie JU: VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997, 277: 396\u2013404.","journal-title":"Methods Enzymol"},{"issue":"5","key":"1717_CR7","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1110\/ps.0236803","volume":"12","author":"B Wallner","year":"2003","unstructured":"Wallner B, Elofsson A: Can correct protein models be identified? Protein Sci 2003, 12(5):1073\u20131086. 10.1110\/ps.0236803","journal-title":"Protein Sci"},{"issue":"10","key":"1717_CR8","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.1089\/cmb.2005.12.1316","volume":"12","author":"SC Tosatto","year":"2005","unstructured":"Tosatto SC: The victor\/FRST function for model quality estimation. J Comput Biol 2005, 12(10):1316\u20131327. 10.1089\/cmb.2005.12.1316","journal-title":"J Comput Biol"},{"issue":"17","key":"1717_CR9","doi-asserted-by":"publisher","first-page":"3509","DOI":"10.1093\/bioinformatics\/bti540","volume":"21","author":"CS Pettitt","year":"2005","unstructured":"Pettitt CS, McGuffin LJ, Jones DT: Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 2005, 21(17):3509\u20133515. 10.1093\/bioinformatics\/bti540","journal-title":"Bioinformatics"},{"key":"1717_CR10","unstructured":"CAFASP4[\n                    http:\/\/fischerlab.cse.buffalo.edu\/CAFASP\/\n                    \n                  ]"},{"key":"1717_CR11","unstructured":"CASP7[\n                    http:\/\/predictioncenter.org\/casp7\/\n                    \n                  ]"},{"issue":"1","key":"1717_CR12","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1093\/bioinformatics\/17.1.63","volume":"17","author":"LJ McGuffin","year":"2001","unstructured":"McGuffin LJ, Bryson K, Jones DT: What are the baselines for protein fold recognition? Bioinformatics 2001, 17(1):63\u201372. 10.1093\/bioinformatics\/17.1.63","journal-title":"Bioinformatics"},{"issue":"7","key":"1717_CR13","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1093\/bioinformatics\/btg097","volume":"19","author":"LJ McGuffin","year":"2003","unstructured":"McGuffin LJ, Jones DT: Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2003, 19(7):874\u2013881. 10.1093\/bioinformatics\/btg097","journal-title":"Bioinformatics"},{"key":"1717_CR14","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1002\/prot.20731","volume":"61 Suppl 7","author":"DT Jones","year":"2005","unstructured":"Jones DT, Bryson K, Coleman A, McGuffin LJ, Sadowski MI, Sodhi JS, Ward JJ: Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins 2005, 61 Suppl 7: 143\u2013151. 10.1002\/prot.20731","journal-title":"Proteins"},{"key":"1717_CR15","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1002\/prot.10536","volume":"53 Suppl 6","author":"B Wallner","year":"2003","unstructured":"Wallner B, Fang H, Elofsson A: Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 2003, 53 Suppl 6: 534\u2013541. 10.1002\/prot.10536","journal-title":"Proteins"},{"issue":"7","key":"1717_CR16","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1110\/ps.062095806","volume":"15","author":"D Eramian","year":"2006","unstructured":"Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA: A composite score for predicting errors in protein structure models. Protein Sci 2006, 15(7):1653\u20131666. 10.1110\/ps.062095806","journal-title":"Protein Sci"},{"issue":"7","key":"1717_CR17","doi-asserted-by":"publisher","first-page":"2302","DOI":"10.1093\/nar\/gki524","volume":"33","author":"Y Zhang","year":"2005","unstructured":"Zhang Y, Skolnick J: TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005, 33(7):2302\u20132309. 10.1093\/nar\/gki524","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1717_CR18","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1110\/ps.9.7.1399","volume":"9","author":"R Samudrala","year":"2000","unstructured":"Samudrala R, Levitt M: Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000, 9(7):1399\u20131401.","journal-title":"Protein Sci"},{"issue":"2","key":"1717_CR19","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1006\/jmbi.1996.0256","volume":"258","author":"B Park","year":"1996","unstructured":"Park B, Levitt M: Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996, 258(2):367\u2013392. 10.1006\/jmbi.1996.0256","journal-title":"J Mol Biol"},{"issue":"1","key":"1717_CR20","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1006\/jmbi.2000.3835","volume":"300","author":"Y Xia","year":"2000","unstructured":"Xia Y, Huang ES, Levitt M, Samudrala R: Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol 2000, 300(1):171\u2013185. 10.1006\/jmbi.2000.3835","journal-title":"J Mol Biol"},{"issue":"1","key":"1717_CR21","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/S0022-2836(03)00323-1","volume":"329","author":"C Keasar","year":"2003","unstructured":"Keasar C, Levitt M: A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol 2003, 329(1):159\u2013174. 10.1016\/S0022-2836(03)00323-1","journal-title":"J Mol Biol"},{"key":"1717_CR22","unstructured":"MQAP Downloads[\n                    http:\/\/cafasp4.cse.buffalo.edu\/progs\/mqaps\/\n                    \n                  ]"},{"key":"1717_CR23","unstructured":"CASP7 Results[\n                    http:\/\/www.predictioncenter.org\/casp\/casp7\/public\/cgi-bin\/results.cgi\n                    \n                  ]"},{"issue":"2","key":"1717_CR24","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","volume":"292","author":"DT Jones","year":"1999","unstructured":"Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195\u2013202. 10.1006\/jmbi.1999.3091","journal-title":"J Mol Biol"},{"issue":"12","key":"1717_CR25","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577\u20132637. 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"issue":"4","key":"1717_CR26","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1002\/prot.20264","volume":"57","author":"Y Zhang","year":"2004","unstructured":"Zhang Y, Skolnick J: Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57(4):702\u2013710. 10.1002\/prot.20264","journal-title":"Proteins"},{"key":"1717_CR27","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1186\/1471-2105-7-288","volume":"7","author":"LJ McGuffin","year":"2006","unstructured":"McGuffin LJ, Smith RT, Bryson K, Sorensen SA, Jones DT: High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics 2006, 7: 288. 10.1186\/1471-2105-7-288","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"1717_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410.","journal-title":"J Mol Biol"},{"issue":"8","key":"1717_CR29","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1093\/bioinformatics\/btg124","volume":"19","author":"K Ginalski","year":"2003","unstructured":"Ginalski K, Elofsson A, Fischer D, Rychlewski L: 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003, 19(8):1015\u20131018. 10.1093\/bioinformatics\/btg124","journal-title":"Bioinformatics"},{"key":"1717_CR30","unstructured":"CASP7 Server Models[\n                    http:\/\/www.predictioncenter.org\/casp7\/SERVER_HTML\/tarballs\/\n                    \n                  ]"},{"issue":"9","key":"1717_CR31","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1093\/bioinformatics\/16.9.776","volume":"16","author":"N Siew","year":"2000","unstructured":"Siew N, Elofsson A, Rychlewski L, Fischer D: MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000, 16(9):776\u2013785. 10.1093\/bioinformatics\/16.9.776","journal-title":"Bioinformatics"},{"key":"1717_CR32","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W","volume":"Suppl 3","author":"A Zemla","year":"1999","unstructured":"Zemla A, Venclovas C, Moult J, Fidelis K: Processing and analysis of CASP3 protein structure predictions. Proteins 1999, Suppl 3: 22\u201329. \n                    Publisher Full Text\n                    \n                   10.1002\/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W","journal-title":"Proteins"},{"key":"1717_CR33","unstructured":"The ModFOLD server[\n                    http:\/\/www.biocentre.rdg.ac.uk\/bioinformatics\/ModFOLD\/\n                    \n                  ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-345.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-345\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-345.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T05:04:01Z","timestamp":1548219841000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-345"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,9,18]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1717"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-345","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,9,18]]},"article-number":"345"}}