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An automated classification of the structure of protein loops.
Oliva B, Bates PA, Querol E, Avilés FX, Sternberg MJ. Oliva B, et al. Among authors: sternberg mj. J Mol Biol. 1997 Mar 7;266(4):814-30. doi: 10.1006/jmbi.1996.0819. J Mol Biol. 1997. PMID: 9102471
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).
Hermoso A, Espadaler J, Enrique Querol E, Aviles FX, Sternberg MJ, Oliva B, Fernandez-Fuentes N. Hermoso A, et al. Among authors: sternberg mj. Bioinform Biol Insights. 2009 Nov 24;1:77-90. Bioinform Biol Insights. 2009. PMID: 20066127 Free PMC article.
Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building.
Adzhubei AA, Sternberg MJ. Adzhubei AA, et al. Among authors: sternberg mj. Protein Sci. 1994 Dec;3(12):2395-410. doi: 10.1002/pro.5560031223. Protein Sci. 1994. PMID: 7756993 Free PMC article.
CAFASP-1: critical assessment of fully automated structure prediction methods.
Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. Fischer D, et al. Among authors: sternberg m. Proteins. 1999;Suppl 3:209-17. doi: 10.1002/(sici)1097-0134(1999)37:3+<209::aid-prot27>3.3.co;2-p. Proteins. 1999. PMID: 10526371
Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.
Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN. Strynadka NC, et al. Among authors: sternberg m. Nat Struct Biol. 1996 Mar;3(3):233-9. doi: 10.1038/nsb0396-233. Nat Struct Biol. 1996. PMID: 8605624
Polyproline-II helix in proteins: structure and function.
Adzhubei AA, Sternberg MJ, Makarov AA. Adzhubei AA, et al. Among authors: sternberg mj. J Mol Biol. 2013 Jun 26;425(12):2100-32. doi: 10.1016/j.jmb.2013.03.018. Epub 2013 Mar 16. J Mol Biol. 2013. PMID: 23507311 Review.
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, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. Jiang Y, et al. Among authors: sternberg mj. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
ArchDB: automated protein loop classification as a tool for structural genomics.
Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX, Sternberg MJ, Oliva B. Espadaler J, et al. Among authors: sternberg mj. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D185-8. doi: 10.1093/nar/gkh002. Nucleic Acids Res. 2004. PMID: 14681390 Free PMC article.
Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.
Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B. Fernandez-Fuentes N, et al. Among authors: sternberg mj. Proteins. 2005 Sep 1;60(4):746-57. doi: 10.1002/prot.20516. Proteins. 2005. PMID: 16021623
Analysis of phenetic trees based on metabolic capabilites across the three domains of life.
Aguilar D, Aviles FX, Querol E, Sternberg MJ. Aguilar D, et al. Among authors: sternberg mj. J Mol Biol. 2004 Jul 9;340(3):491-512. doi: 10.1016/j.jmb.2004.04.059. J Mol Biol. 2004. PMID: 15210350
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