An interactive website with details of the classification taxonomy for DNA-binding motifs can be found
at the address:
http://www.biochem.ucl.ac.uk/bsm/prot_dna/prot_dna_cover.html
Enzyme structural database with enzyme classifications:
http://www.biochem.ucl.ac.uk/bsm/enzymes/ index.html
Molecular graphics movies are particularly useful for illustrating allosteric transitions and proposed
catalytic mechanisms. For instance, the allosteric changes in DNA helicase are shown in an idealized
continuum of the structural states in the movie at:
http://sci.cancerresearchuk.org/labs/wigley/projects/helicase/morph1.html and
http://sci.cancerresearchuk.org/labs/wigley/projects/helicase/morph2.html
A graphics movie showing the catalytic mechanism of AP endonuclease is provided at:
http://www. scripps.edu/jat/
A molecular graphics movie of the bacteriophage DNA pump may be viewed at:
http://bilbo.bio.purdue.edu/viruswww/Rossmann_home/movies.shtml
ProNIT, a database for the thermodynamics of protein–nucleic acid interactions is available at:
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
References
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A-DNA. Proc. Natl. Acad. Sci. USA, 2001, 98 , 7265–7270. - C.R. Calladine and H.R. Drew, A base-centred explanation of the B-to-A transition in DNA. J. Mol.
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factor IIIA from Xenopusoocytes. EMBO J., 1985, 4 , 1609–1614. - Y. Choo and A. Klug, Physical basis of a protein–DNA recognition code. Curr. Opin. Struct. Biol.,
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there no simple code for recognition? J. Mol. Biol., 2000, 301 , 597–624. - P.A. Rice, S. Yang, K. Mizuuchi and H.A. Nash, Crystal structure of an IHF-DNA complex: a
protein-induced DNA U-turn. Cell, 1996, 87 , 1295–1306. - T.W. Lynch, E.K. Read, A.N. Mattis, J.F. Gardner and P.A. Rice, Integration host factor: putting a
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