Protein-DNA recognition patterns and predictions.

@article{citeulike:620752, abstract = {Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.}, address = {Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8520, Japan. sarai@bse.kyutech.ac.jp}, author = {Sarai, A. and Kono, H. }, citeulike-article-id = {620752}, doi = {http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537}, issn = {1056-8700}, journal = {Annu Rev Biophys Biomol Struct}, keywords = {protein\_dna}, pages = {379--398}, posted-at = {2008-07-24 15:43:07}, priority = {2}, title = {Protein-DNA recognition patterns and predictions.}, url = {http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537}, volume = {34}, year = {2005} }

TY - JOUR ID - citeulike:620752 L3 - citeulike-article-id:620752 N2 - Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins. JF - Annu Rev Biophys Biomol Struct SN - 1056-8700 AD - Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8520, Japan. sarai@bse.kyutech.ac.jp EP - 398 TI - Protein-DNA recognition patterns and predictions. VL - 34 SP - 379 KW - protein_dna AU - Sarai, A AU - Kono, H PY - 2005/// UR - http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537 ER -