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The evaluation of protein structure prediction results.
Cozzetto D, Giorgetti A, Raimondo D, Tramontano A. Cozzetto D, et al. Mol Biotechnol. 2008 May;39(1):1-8. doi: 10.1007/s12033-007-9023-6. Epub 2007 Dec 11. Mol Biotechnol. 2008. PMID: 18071927 Review.
Ten years of predictions ... and counting.
Cozzetto D, Di Matteo A, Tramontano A. Cozzetto D, et al. FEBS J. 2005 Feb;272(4):881-2. doi: 10.1111/j.1742-4658.2005.04549.x. FEBS J. 2005. PMID: 15691322 Free article.
The assessment of methods for protein structure prediction.
Tramontano A, Cozzetto D, Giorgetti A, Raimondo D. Tramontano A, et al. Among authors: cozzetto d. Methods Mol Biol. 2008;413:43-57. doi: 10.1007/978-1-59745-574-9_2. Methods Mol Biol. 2008. PMID: 18075161
Evaluation of CASP8 model quality predictions.
Cozzetto D, Kryshtafovych A, Tramontano A. Cozzetto D, et al. Proteins. 2009;77 Suppl 9:157-66. doi: 10.1002/prot.22534. Proteins. 2009. PMID: 19714774
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, S… See abstract for full author list ➔ Jiang Y, et al. Among authors: d andrea d, cozzetto d. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
The PMDB Protein Model Database.
Castrignanò T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. Castrignanò T, et al. Among authors: cozzetto d. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D306-9. doi: 10.1093/nar/gkj105. Nucleic Acids Res. 2006. PMID: 16381873 Free PMC article.
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