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• W2107822010 abstract "The biological functions of DNA-binding proteins often require that they interact with their targets with high affinity and/or high specificity. Here, we describe a computational method that estimates the extent of optimization for affinity and specificity of amino acids at a protein–DNA interface based on the crystal structure of the complex, by modeling the changes in binding-free energy associated with all individual amino acid and base substitutions at the interface. The extent to which residues are predicted to be optimal for specificity versus affinity varies within a given protein–DNA interface and between different complexes, and in many cases recapitulates previous experimental observations. The approach provides a complement to traditional methods of mutational analysis, and should be useful for rapidly formulating hypotheses about the roles of amino acid residues in protein–DNA interfaces." @default.
• W2107822010 created "2016-06-24" @default.
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• W2107822010 date "2009-04-23" @default.
• W2107822010 modified "2023-09-27" @default.
• W2107822010 title "Assessment of the optimization of affinity and specificity at protein–DNA interfaces" @default.
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• W2107822010 doi "https://doi.org/10.1093/nar/gkp242" @default.
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