Shanahan, H P , Garcia, M A , Jones, S and Thornton, J M (2004) Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Research, 32 (16).
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Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix-turn-helix (HTH), helix-hairpin-helix (HhH) and helix-loop-helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif.
This is a Submitted version This version's date is: 2004 This item is not peer reviewed
https://repository.royalholloway.ac.uk/items/e2b0581d-5b7f-9a52-5245-3977335c059f/1/
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