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Items: 1 to 20 of 38

1.

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.

Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W462-8. doi: 10.1093/nar/gkq319. Epub 2010 Apr 30.

2.

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.

3.

Predicting DNA recognition by Cys2His2 zinc finger proteins.

Persikov AV, Osada R, Singh M.

Bioinformatics. 2009 Jan 1;25(1):22-9. doi: 10.1093/bioinformatics/btn580. Epub 2008 Nov 13.

4.

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.

Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF.

Nucleic Acids Res. 2009 Jan;37(Database issue):D279-83. doi: 10.1093/nar/gkn606. Epub 2008 Sep 23.

5.

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.

Liu J, Stormo GD.

Bioinformatics. 2008 Sep 1;24(17):1850-7. doi: 10.1093/bioinformatics/btn331. Epub 2008 Jun 27.

6.

A probabilistic model of local sequence alignment that simplifies statistical significance estimation.

Eddy SR.

PLoS Comput Biol. 2008 May 30;4(5):e1000069. doi: 10.1371/journal.pcbi.1000069.

7.

Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.

Brayer KJ, Segal DJ.

Cell Biochem Biophys. 2008;50(3):111-31. doi: 10.1007/s12013-008-9008-5. Epub 2008 Feb 6. Review.

8.

Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA.

Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE.

J Mol Biol. 2007 Oct 5;372(5):1227-45. Epub 2007 Jul 21.

PMID:
17716689
9.

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

Siggers TW, Honig B.

Nucleic Acids Res. 2007;35(4):1085-97. Epub 2007 Jan 30.

10.

Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA.

Segal DJ, Crotty JW, Bhakta MS, Barbas CF 3rd, Horton NC.

J Mol Biol. 2006 Oct 20;363(2):405-21. Epub 2006 Aug 11.

11.

Weight matrices for protein-DNA binding sites from a single co-crystal structure.

Endres RG, Wingreen NS.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):061921. Epub 2006 Jun 28.

PMID:
16906878
12.

Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases.

Mandell JG, Barbas CF 3rd.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W516-23.

13.

Ab initio prediction of transcription factor targets using structural knowledge.

Kaplan T, Friedman N, Margalit H.

PLoS Comput Biol. 2005 Jun;1(1):e1. Epub 2005 Jun 24.

14.
15.

Predicting specificity in bZIP coiled-coil protein interactions.

Fong JH, Keating AE, Singh M.

Genome Biol. 2004;5(2):R11. Epub 2004 Jan 16.

16.

TRANSFAC: transcriptional regulation, from patterns to profiles.

Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E.

Nucleic Acids Res. 2003 Jan 1;31(1):374-8.

17.

Probabilistic code for DNA recognition by proteins of the EGR family.

Benos PV, Lapedes AS, Stormo GD.

J Mol Biol. 2002 Nov 1;323(4):701-27.

PMID:
12419259
18.

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes.

Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO.

Structure. 2001 Aug;9(8):717-23.

19.

Three classes of C2H2 zinc finger proteins.

Iuchi S.

Cell Mol Life Sci. 2001 Apr;58(4):625-35. Review.

PMID:
11361095
20.

The sequence of the human genome.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995

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