Rosario I. Corona

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BACKGROUND 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(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)
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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