{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:43:07Z","timestamp":1706812987023},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,3,21]],"date-time":"2015-03-21T00:00:00Z","timestamp":1426896000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0526-z","type":"journal-article","created":{"date-parts":[[2015,3,20]],"date-time":"2015-03-20T03:33:42Z","timestamp":1426822422000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest"],"prefix":"10.1186","volume":"16","author":[{"given":"Juyong","family":"Lee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiho","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"InSuk","family":"Joung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keehyoung","family":"Joo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernard R","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jooyoung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,3,21]]},"reference":[{"issue":"7","key":"526_CR1","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","volume":"21","author":"J S\u00f6ding","year":"2005","unstructured":"S\u00f6ding J. Protein homology detection by HMM\u2013HMM comparison. Bioinformatics. 2005; 21(7):951\u201360.","journal-title":"Bioinformatics"},{"issue":"S9","key":"526_CR2","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1002\/prot.22499","volume":"77","author":"A Hildebrand","year":"2009","unstructured":"Hildebrand A, Remmert M, Biegert A, S\u00f6ding J. Fast and accurate automatic structure prediction with hhpred. Proteins: Struct, Funct, Bioinf. 2009; 77(S9):128\u201332.","journal-title":"Proteins: Struct, Funct, Bioinf."},{"key":"526_CR3","volume-title":"Research in Computational Molecular Biology","author":"J Peng","year":"2009","unstructured":"Peng J, Xu J. Boosting protein threading accuracy. In: Research in Computational Molecular Biology. Heidelberg: Springer Berlin: 2009. p. 31\u201345. http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-642-02008-7_3# #."},{"issue":"S10","key":"526_CR4","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1002\/prot.23175","volume":"79","author":"J Peng","year":"2011","unstructured":"Peng J, Xu J. RaptorX: Exploiting structure information for protein alignment by statistical inference. Proteins: Struct Funct Bioinf. 2011; 79(S10):161\u201371.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"2","key":"526_CR5","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1002\/prot.21945","volume":"72","author":"S Wu","year":"2008","unstructured":"Wu S, Zhang Y. MUSTER: improving protein sequence profile\u2013profile alignments by using multiple sources of structure information. Proteins: Struct Funct Bioinf. 2008; 72(2):547\u201356.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"15","key":"526_CR6","doi-asserted-by":"publisher","first-page":"2076","DOI":"10.1093\/bioinformatics\/btr350","volume":"27","author":"Y Yang","year":"2011","unstructured":"Yang Y, Faraggi E, Zhao H, Zhou Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics. 2011; 27(15):2076\u201382.","journal-title":"Bioinformatics"},{"issue":"10","key":"526_CR7","doi-asserted-by":"publisher","first-page":"4813","DOI":"10.1529\/biophysj.108.129684","volume":"95","author":"K Joo","year":"2008","unstructured":"Joo K, Lee J, Kim I, Lee SJ, Lee J. Multiple sequence alignment by conformational space annealing. Bioph J. 2008; 95(10):4813\u20139.","journal-title":"Bioph J."},{"issue":"7","key":"526_CR8","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1093\/bioinformatics\/btm017","volume":"23","author":"J Pei","year":"2007","unstructured":"Pei J, Grishin NV. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics. 2007; 23(7):802\u20138.","journal-title":"Bioinformatics"},{"issue":"suppl 2","key":"526_CR9","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1093\/nar\/gkl092","volume":"34","author":"F Armougom","year":"2006","unstructured":"Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, et al.Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 2006; 34(suppl 2):604\u20138.","journal-title":"Nucleic Acids Res."},{"issue":"S9","key":"526_CR10","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1002\/prot.22561","volume":"77","author":"D Cozzetto","year":"2009","unstructured":"Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins: Struct Funct Bioinf. 2009; 77(S9):18\u201328.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"S10","key":"526_CR11","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1002\/prot.23177","volume":"79","author":"V Mariani","year":"2011","unstructured":"Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T. Assessment of template based protein structure predictions in CASP9. Proteins: Struct Funct Bioinf. 2011; 79(S10):37\u201358.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"S10","key":"526_CR12","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1002\/prot.23182","volume":"79","author":"A Kryshtafovych","year":"2011","unstructured":"Kryshtafovych A, Fidelis K, Moult J. CASP9 results compared to those of previous casp experiments. Proteins: Struct Funct Bioinf. 2011; 79(S10):196\u2013207.","journal-title":"Proteins: Struct Funct Bioinf."},{"key":"526_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/prot.24452","volume":"82","author":"J Moult","year":"2014","unstructured":"Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins: Struct Funct Bioinf. 2014; 82:1\u20136. doi:10.1002\/prot.24452.","journal-title":"Proteins: Struct Funct Bioinf."},{"key":"526_CR14","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1002\/prot.24489","volume":"82","author":"A Kryshtafovych","year":"2014","unstructured":"Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, et al.Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins: Struct Funct Bioinf. 2014; 82:26\u201342. doi:10.1002\/prot.24489.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"S8","key":"526_CR15","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1002\/prot.21628","volume":"69","author":"K Joo","year":"2007","unstructured":"Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins: Struct Funct Bioinf. 2007; 69(S8):83\u20139.","journal-title":"Proteins: Struct Funct Bioinf."},{"key":"526_CR16","first-page":"86","volume":"64","author":"A Sali","year":"1994","unstructured":"Sali A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. Protein Struct Distance Anal. 1994; 64:86.","journal-title":"Protein Struct Distance Anal."},{"key":"526_CR17","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1016\/S0076-6879(03)74020-8","volume":"374","author":"A Fiser","year":"2003","unstructured":"Fiser A, \u0160ali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 2003; 374:461\u201391.","journal-title":"Methods Enzymol."},{"issue":"S9","key":"526_CR18","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1002\/prot.22570","volume":"77","author":"E Krieger","year":"2009","unstructured":"Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, et al.Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Struct Funct Bioinf. 2009; 77(S9):114\u201322.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"S9","key":"526_CR19","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1002\/prot.22567","volume":"77","author":"J Xu","year":"2009","unstructured":"Xu J, Peng J, Zhao F. Template-based and free modeling by RAPTOR++ in CASP8. Proteins: Struct Funct Bioinf. 2009; 77(S9):133\u20137.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"4","key":"526_CR20","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1002\/prot.22312","volume":"75","author":"K Joo","year":"2009","unstructured":"Joo K, Lee J, Seo JH, Lee K, Kim BG, Lee J. All-atom chain-building by optimizing modeller energy function using conformational space annealing. Proteins: Struct Funct Bioinf. 2009; 75(4):1010\u201323.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"Suppl 2(April","key":"526_CR21","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1002\/prot.24397","volume":"82","author":"K Joo","year":"2014","unstructured":"Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, et al.Protein structure modeling for CASP10 by multiple layers of global optimization. Proteins: Struct Funct Bioinf. 2014; 82(Suppl 2(April)):188\u201395.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"8","key":"526_CR22","doi-asserted-by":"publisher","first-page":"2380","DOI":"10.1002\/prot.23046","volume":"79","author":"J Thompson","year":"2011","unstructured":"Thompson J, Baker D. Incorporation of evolutionary information into rosetta comparative modeling. Proteins: Struct Funct Bioinf. 2011; 79(8):2380\u20138.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"1","key":"526_CR23","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman L. Random forests. Mach Learn. 2001; 45(1):5\u201332.","journal-title":"Mach Learn."},{"issue":"4","key":"526_CR24","doi-asserted-by":"publisher","first-page":"60372","DOI":"10.1371\/journal.pone.0060372","volume":"8","author":"J Lee","year":"2013","unstructured":"Lee J, Lee J. Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction. PLoS ONE. 2013; 8(4):60372.","journal-title":"PLoS ONE"},{"key":"526_CR25","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1038\/srep02197","volume":"3","author":"J Lee","year":"2013","unstructured":"Lee J, Gross SP, Lee J. Improved network community structure improves function prediction. Sci Rep. 2013; 3:2197.","journal-title":"Sci Rep."},{"issue":"1","key":"526_CR26","first-page":"55","volume":"4","author":"A Ziegler","year":"2014","unstructured":"Ziegler A, K\u00f6nig IR. Mining data with random forests: current options for real-world applications. Wiley Interdiscip Rev: Data Min Knowl Discov. 2014; 4(1):55\u201363.","journal-title":"Wiley Interdiscip Rev: Data Min Knowl Discov."},{"issue":"9","key":"526_CR27","doi-asserted-by":"publisher","first-page":"106542","DOI":"10.1371\/journal.pone.0106542","volume":"9","author":"B Manavalan","year":"2014","unstructured":"Manavalan B, Lee J, Lee J. Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PLoS ONE. 2014; 9(9):106542.","journal-title":"PLoS ONE"},{"key":"526_CR28","volume-title":"Proceedings of the 25th International Conference on Machine Learning. ICML \u201908","author":"R Caruana","year":"2008","unstructured":"Caruana R, Karampatziakis N, Yessenalina A. An empirical evaluation of supervised learning in high dimensions. In: Proceedings of the 25th International Conference on Machine Learning. ICML \u201908. New York, NY, USA: ACM: 2008. p. 96\u2013103."},{"issue":"4","key":"526_CR29","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\u201310.","journal-title":"Proteins"},{"issue":"21","key":"526_CR30","doi-asserted-by":"publisher","first-page":"2722","DOI":"10.1093\/bioinformatics\/btt473","volume":"29","author":"V Mariani","year":"2013","unstructured":"Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics (Oxford, England). 2013; 29(21):2722\u20138.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"12","key":"526_CR31","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","volume":"19","author":"G Wang","year":"2003","unstructured":"Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics. 2003; 19(12):1589\u201391.","journal-title":"Bioinformatics"},{"issue":"S8","key":"526_CR32","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/prot.21753","volume":"69","author":"J Kopp","year":"2007","unstructured":"Kopp J, Bordoli L, Battey JND, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins: Struct Funct Bioinf. 2007; 69(S8):38\u201356.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"1","key":"526_CR33","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1002\/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F","volume":"41","author":"TN Petersen","year":"2000","unstructured":"Petersen TN, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, et al.Prediction of protein secondary structure at 80% accuracy. Proteins: Struct Funct Bioinf. 2000; 41(1):17\u201320.","journal-title":"Proteins: Struct Funct Bioinf."},{"issue":"7","key":"526_CR34","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1002\/prot.24074","volume":"80","author":"K Joo","year":"2012","unstructured":"Joo K, Lee SJ, Lee J. SANN: solvent accessibility prediction of proteins by nearest neighbor method. Proteins: Struct Funct Bioinf. 2012; 80(7):1791\u20137.","journal-title":"Proteins: Struct Funct Bioinf."},{"key":"526_CR35","volume-title":"Classification and regression trees. Statistics\/Probability Series","author":"L Breiman","year":"1984","unstructured":"Breiman L, Friedman JH, Olshen RA, Stone CJ. Classification and regression trees. Statistics\/Probability Series. Belmont, California, USA: Wadsworth Publishing Company; 1984."},{"issue":"1","key":"526_CR36","first-page":"81","volume":"1","author":"JR Quinlan","year":"1986","unstructured":"Quinlan JR. Induction of decision trees. Mach Learn. 1986; 1(1):81\u2013106.","journal-title":"Mach Learn."},{"issue":"9","key":"526_CR37","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","volume":"9","author":"A Fiser","year":"2000","unstructured":"Fiser A, Do RKG, Sali A. Modeling of loops in protein structures. Protein Sci. 2000; 9(9):1753\u201373. doi:10.1110\/ps.9.9.1753.","journal-title":"Protein Sci."},{"issue":"1","key":"526_CR38","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1002\/prot.340100104","volume":"10","author":"A Pastore","year":"1991","unstructured":"Pastore A, Atkinson RA, Saudek V, Williams RJ. Topological mirror images in protein structure computation: an underestimated problem. Proteins. 1991; 10(1):22\u201332.","journal-title":"Proteins"},{"issue":"10","key":"526_CR39","doi-asserted-by":"publisher","first-page":"5482","DOI":"10.1073\/pnas.96.10.5482","volume":"96","author":"A Liwo","year":"1999","unstructured":"Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA. Protein structure prediction by global optimization of a potential energy function. Proc Nat Acad Sci USA. 1999; 96(10):5482\u20135.","journal-title":"Proc Nat Acad Sci USA."},{"issue":"18","key":"526_CR40","doi-asserted-by":"publisher","first-page":"10125","DOI":"10.1073\/pnas.181328398","volume":"98","author":"D Kihara","year":"2001","unstructured":"Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Nat Acad Sci USA. 2001; 98(18):10125\u201330.","journal-title":"Proc Nat Acad Sci USA."},{"issue":"Suppl 9(August","key":"526_CR41","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1002\/prot.22588","volume":"77","author":"Y Zhang","year":"2009","unstructured":"Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins. 2009; 77(Suppl 9(August)):100\u201313. doi:10.1002\/prot.22588.","journal-title":"Proteins"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0526-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0526-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0526-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0526-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T01:35:00Z","timestamp":1598837700000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0526-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,21]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["526"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0526-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,21]]},"assertion":[{"value":"17 September 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 March 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 March 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"94"}}