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Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

By Huiying Zhao, Yuedong Yang and Yaoqi Zhou


Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein–DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state

Topics: Original Papers
Publisher: Oxford University Press
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Provided by: PubMed Central
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