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DNA binding sites are specific regions of the genome where proteins interact with the double helix to regulate essential cellular processes such as transcription, replication, and repair. These interactions are mediated by the complementarity between the surface topology of DNA-binding proteins (transcription factors) and the chemical structure of the DNA major and minor grooves. This paper reviews the biophysical mechanisms of DNA-protein recognition, the role of motif models such as Position Weight Matrices (PWMs), and modern computational approaches for identifying binding sites genome-wide. dubbindosite link

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