Rosario I. Corona

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Structural insight from transcription factor-DNA (TF-DNA) complexes is of paramount importance to our understanding of the affinity and specificity of TF-DNA interaction, and to the development of structure-based prediction of TF binding sites. Yet the majority of the TF-DNA complexes remain unsolved despite the considerable experimental efforts being made.(More)
MOTIVATION Computational modeling of protein-DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein-DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we(More)
DNA-binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific (HS) to nonspecific (NS). Alterations of DNA-binding specificity, due to either genetic variation or somatic mutations, can(More)
This paper presents a brief description of the protein side chain packing problem (PSCPP) and a performance assessment, on this problem, of three state-of-the-art algorithms: SCWRL4, OPUS-Rota, and CIS-RR. In order to perform a fair comparison, the algorithms are evaluated on three data sets, two of them were previously proposed in the literature and a set(More)
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