Recognition Rules for Binding of Homeodomains to Operator DNA

References

• Kalthoff , K. 1996 . Analysis of Biological Development. 546 New York : McGraw-Hill . p.
   Google Scholar
• Svingen , T. and Koopman , P. 2007 . Sex Dev , 1 : 12 – 23 .
   PubMed Web of Science ®Google Scholar
• Wigle , J. T. and Eisenstat , D. D. 2008 . Clin Genet , 73 : 212 – 226 .
   PubMed Web of Science ®Google Scholar
• Gehring , W. J. , Affolter , M. and Bürglin , T. 1994 . Annu Rev Biochem , 63 : 487 – 526 .
   PubMed Web of Science ®Google Scholar
• Derelle , R. , Lopez , P. , Le Guyader , H. and Manuel , M. 2007 . Evol Dev , 9 : 212 – 219 .
   PubMed Web of Science ®Google Scholar
• Kissinger , C. R. , Liu , B. , Martin-Blanco , E. , Kornberg , T. B. and Pabo , C. O. 1990 . Cell , 63 : 579 – 590 .
   PubMed Web of Science ®Google Scholar
• Rubin , G. M. , Yandell , M. D. and Wortman , J. R. 2000 . et al. Science , 287 : 2204 – 2215 .
   PubMed Web of Science ®Google Scholar
• Ledneva , R. K. , Alexeevskii , A. V. , Vasil'ev , S. A. , Spirin , S. A. and Karyagina , A. S. 2001 . Mol Biol , 35 : 647 – 659 .
   Web of Science ®Google Scholar
• Nadassy , K. , Wodak , S. J. and Janin , J. 1999–2017 . Biochemistry , 38 1999.
   PubMed Web of Science ®Google Scholar
• Mandel-Gutfreund , Y. , Schueler , O. and Margalit , H. 1995 . J Mol Biol , 253 : 370 – 382 .
   PubMed Web of Science ®Google Scholar
• Luscombe , N. M. , Laskowski , R. A. and Thornton , J. M. 1997 . Nucleic Acids Res , 25 : 4940 – 4945 .
   PubMed Web of Science ®Google Scholar
• Luscombe , N. M. , Laskowski , R. A. and Thornton , J. M. 2001 . Nucleic Acids Res , 29 : 2860 – 2874 .
   PubMed Web of Science ®Google Scholar
• Jones , S. , Heyningen , P. , Berman , H. M. and Thornton , J. M. 1999 . J Mol Biol , 287 : 877 – 896 .
   PubMed Web of Science ®Google Scholar
• Jones , S. , Shanahan , H. P. , Berman , H. M. and Thornton , J. M. 2003 . Nucleic Acids Res , 31 : 7189 – 7198 .
   PubMed Web of Science ®Google Scholar
• Shanahan , H. P. , Garcia , M. A. , Jones , S. and Thornton , J. M. 2004 . Nucleic Acids Res , 32 : 4732 – 4741 .
   PubMed Web of Science ®Google Scholar
• Tsuchiya , Y. , Kinoshita , K. and Nakamura , H. 2004 . Proteins , 55 : 885 – 894 .
   PubMed Web of Science ®Google Scholar
• Liu , Z. , Mao , F. , Guo , J. , Yan , B. , Wang , P. , Qu , Y. and Xu , Y. 2005 . Nucleic Acids Res , 33 : 546 – 558 .
   PubMed Web of Science ®Google Scholar
• Szilagyi , A. and Skolnick , J. 2006 . J Mol Biol , 358 : 922 – 933 .
   PubMed Web of Science ®Google Scholar
• Stawiski , E. W. , Gregoret , L. M. and Mandel-Gutfreund , Y. 2003 . J Mol Biol , 306 : 1065 – 1079 .
   Web of Science ®Google Scholar
• Samanta , S. , Chakrabarti , J. and Bhattacharyya , D. 2010 . J Biomol Struct Dyn , 27 : 429 – 442 .
   PubMed Web of Science ®Google Scholar
• Carra , C. and Cucinotta , F. A. 2010 . J Biomol Struct Dyn , 27 : 407 – 427 .
   PubMed Web of Science ®Google Scholar
• Roy , S. and Thakur , A. R. 2011 . J Biomol Struct Dyn , 28 : 729 – 742 .
   PubMed Web of Science ®Google Scholar
• Rohs , R. 2011 . J Biomol Struct Dyn , 28 : 1152 – 1152 .
   Google Scholar
• Liu , P. , Rohs , R. , Mann , R. and Honig , B. 2011 . J Biomol Struct Dyn , 28 : 1155 – 1155 .
   Web of Science ®Google Scholar
• Roy , S. and Thakur , A. R. 2010 . J Biomol Struct Dyn , 27 : 443 – 455 .
   PubMed Web of Science ®Google Scholar
• Chirgadze , Yu. N. and Tabolina , O. Y. 1996 . Protein Eng , 9 : 745 – 754 .
   PubMedGoogle Scholar
• Chirgadze , Yu. N. and Larionova , E. A. 1999 . Protein Eng , 12 : 101 – 105 .
   PubMedGoogle Scholar
• Chirgadze , Yu. N. and Larionova , E. A. 2001 . Mol Biol (Moscow) , 35 : 709 – 716 .
   Web of Science ®Google Scholar
• Chirgadze , Yu. N. and Larionova , E. A. 2003 . Mol Biol (Moscow) , 37 : 232 – 239 .
   Web of Science ®Google Scholar
• Chirgadze , Yu. N. and Larionova , E. A. 2005 . Mol Biol (Moscow) , 39 : 892 – 905 .
   Google Scholar
• Chirgadze , Yu. N. , Larionova , E. A. and Ivanov , V. V. 2009 . J Biomol Struct Dyn , 27 : 83 – 95 .
   PubMed Web of Science ®Google Scholar
• Chirgadze , Yu. N. , Zheltukhin , E. I. , Polozov , R. V. , Sivozhelezov , V. S. and Ivanov , V. V. 2009 . J Biomol Struct Dyn , 26 : 687 – 700 .
   PubMed Web of Science ®Google Scholar
• Matthews , B. W. 1988 . Nature , 335 : 294 – 295 .
   PubMed Web of Science ®Google Scholar
• Suzuki , M. , Brenner , S. E. , Gerstein , M. and Yagi , N. 1995 . Protein Eng , 8 : 319 – 328 .
   PubMedGoogle Scholar
• Choo , Y. and Klug , A. 1997 . Curr Opin Struct Biol , 7 : 117 – 125 .
   PubMed Web of Science ®Google Scholar
• Benos , P. V. , Lapedes , A. S. and Stormo , G. D. 2002 . Bioessays , 24 : 466 – 475 .
   PubMed Web of Science ®Google Scholar
• Murzin , A. G. , Brenner , S. E. , Hubbard , T. and Chothia , C. 1995 . J Mol Biol , 247 : 536 – 540 .
   PubMed Web of Science ®Google Scholar
• Travers , A. , Hiriart , E. , Churcher , M. , Caserta , M. and Di Mauro , E. 2010 . J Biomol Struct Dyn , 27 : 713 – 724 .
   PubMed Web of Science ®Google Scholar
• Xu , F. and Olson , W. K. 2010 . J Biomol Struct Dyn , 27 : 725 – 739 .
   PubMed Web of Science ®Google Scholar
• Trifonov , E. N. 2010 . J Biomol Struct Dyn , 27 : 741 – 746 .
   PubMed Web of Science ®Google Scholar
• De Santis , P. , Morosetti , S. and Scipioni , A. 2010 . J Biomol Struct Dyn , 27 : 747 – 764 .
   PubMed Web of Science ®Google Scholar
• Babbitt , G. A. , Tolstorukov , M. Y. and Kim , Y. 2010 . J Biomol Struct Dyn , 27 : 765 – 780 .
   PubMed Web of Science ®Google Scholar
• Clark , D. J. 2010 . J Biomol Struct Dyn , 27 : 781 – 793 .
   PubMed Web of Science ®Google Scholar
• Johnson , S. M. 2010 . J Biomol Struct Dyn , 27 : 795 – 802 .
   PubMed Web of Science ®Google Scholar
• Arya , G. , Maitra , A. and Grigoryev , S. A. 2010 . J Biomol Struct Dyn , 27 : 803 – 820 .
   PubMed Web of Science ®Google Scholar
• Cui , F. and Zhurkin , V. B. 2010 . J Biomol Struct Dyn , 27 : 821 – 841 .
   PubMed Web of Science ®Google Scholar
• Wang , D. , Ulyanov , N. B. and Zhurkin , V. B. 2010 . J Biomol Struct Dyn , 27 : 843 – 859 .
   PubMed Web of Science ®Google Scholar
• West , S. M. , Rohs , R. , Mann , R. S. and Honing , B. 2010 . J Biomol Struct Dyn , 27 : 861 – 866 .
   PubMed Web of Science ®Google Scholar
• Sereda , V. and Bishop , T. C. 2010 . J Biomol Struct Dyn , 27 : 867 – 887 .
   PubMed Web of Science ®Google Scholar
• Suzuki , M. and Yagi , N. 1994 . Proc Natl Acad Sci USA , 91 : 12357 – 12361 .
   PubMed Web of Science ®Google Scholar
• Suzuki , M. 1995 . Protein Eng , 8 : 1 – 4 .
   PubMedGoogle Scholar
• Pellizzari , L. , Fabbro , D. , Lonigro , R. , Di Lauro , R. and Damante , G. 1996 . Biochem J , 315 : 363 – 367 .
   PubMed Web of Science ®Google Scholar
• Joshi , R. , Passner , J. M. , Rohs , R. , Jain , R. , Sosinsky , A. , Crickmore , M. A. , Jacob , V. , Aggarwal , A. K. , Honig , B. and Mann , R. S. 2007 . Cell , 131 : 530 – 543 .
   PubMed Web of Science ®Google Scholar
• Tolstorukov , M. Y. , Jernigan , R. L. and Zhurkin , V. B. 2004 . J Mol Biol , 337 : 65 – 76 .
   PubMed Web of Science ®Google Scholar
• Pabo , C. O. and Nekludova , L. 2000 . J Mol Biol , 301 : 597 – 624 .
   PubMed Web of Science ®Google Scholar
• Berman , H. M. , Olson , W. K. , Beveridge , D. L. , Westbrook , J. , Gelbin , A. and Demeny , T. 1992 . Nucleic Acid Database. . Biophys J , 63 : 751 – 759 .
   PubMed Web of Science ®Google Scholar
• Berman , H. M. , Westbrook , J. , Feng , Z. , Gilliland , G. , Bhat , T. N. , Weissig , H. , Shindyalov , I. N. and Bourne , P. E. 2000 . The RCSB Protein Data Bank. . Nucleic Acids Res , 28 : 235 – 242 . www.pdb.org.
   PubMed Web of Science ®Google Scholar
• Kaplan , W. and Littlejohn , T. G. 2001 . Brief Bioinform , 2 : 195 – 197 .
   PubMedGoogle Scholar
• Hovde , S. , Abate-Shen , C. and Geiger , J. H. 2001 . Biochemistry , 40 : 12013 – 12021 .
   PubMed Web of Science ®Google Scholar
• Koradi , R. , Billeter , M. and Wüthrich , K. 1996 . J Mol Graph , 14 : 51 – 55 . 29–32
   PubMedGoogle Scholar
• Finn , R. D. , Tate , J. , Mistry , J. , Coggill , P. C. , Sammut , S. J. , Hotz , H. R. , Ceric , G. , Forslund , K. , Eddy , S. R. , Sonnhammer , E. L. and Bateman , A. 2008 . Nucleic Acids Res , 36 : D281 – D288 .
   PubMed Web of Science ®Google Scholar
• Shoemaker , B. A. , Zhang , D. , Thangudu , R. R. , Tyagi , M. , Fong , J. H. , Marchler-Bauer , A. , Bryant , S. H. , Madej , T. and Panchenko , A. R. 2010 . Nucleic Acids Res , 38 : D518 – D524 .
   PubMed Web of Science ®Google Scholar
• An , J. , Nakama , T. , Kubota , Y. and Sarai , A. 1998 . Bioinformatics , 14 : 188 – 195 .
   PubMed Web of Science ®Google Scholar
• Birrane , G. , Soni , A. and Ladias , J. A. 2009 . Biochemistry , 48 : 1148 – 1155 .
   PubMed Web of Science ®Google Scholar
• Iyaguchi , D. , Yao , M. , Watanabe , N. , Nishihira , J. and Tanaka , I. 2007 . Structure , 15 : 75 – 83 .
   PubMed Web of Science ®Google Scholar
• Cherstvy , A. G. 2009 . J Phys Chem B , 113 : 4242 – 4247 .
   PubMed Web of Science ®Google Scholar
• Rohs , R. , West , S. M. , Sosinsky , A. , Liu , P. , Mann , R. S. and Honig , B. 2009 . Nature , 461 : 1248 – 1253 .
   PubMed Web of Science ®Google Scholar
• Siggers , T. W. , Silkov , A. and Honig , B. 2005 . J Mo Biol , 345 : 1027 – 1045 .
   PubMed Web of Science ®Google Scholar
• Berger , M. F. , Badis , G. , Gehrke , A. R. , Talukder , S. , Philippakis , A. A. , Peña-Castillo , L. , Alleyne , T. M. , Mnaimneh , S. , Botvinnik , O. B. , Chan , E. T. , Khalid , F. , Zhang , W. , Newburger , D. , Jaeger , S. A. , Morris , Q. D. , Bulyk , M. L. and Hughes , T. R. 2008 . Cell , 133 : 1266 – 1276 .
   PubMed Web of Science ®Google Scholar
• Noyes , M. B. , Christensen , R. G. , Wakabayashi , A. , Stormo , G. D. , Brodsky , M. H. and Wolfe , S. A. 2008 . Cell , 133 : 1277 – 1289 .
   PubMed Web of Science ®Google Scholar
• Privalov , P. L. , Dragan , A. I. and Crane-Robinson , C. 2011 . Nucleic Acids Res , 39 : 2483 – 2491 .
   PubMed Web of Science ®Google Scholar