Abstract. The coiled-coil protein domain is a widespread structural motif known to be involved in a wealth of key interactions in cells and organisms. Coiled-coil recognition and prediction of their location in a protein sequence are important steps for modeling protein structure and function. Nowadays, thanks to the increasing number of experimentally determined protein structures, a significant number of coiled-coil protein domains is available. This enables the development of methods suited to predict the coiled-coil structural motifs starting from the protein sequence. Several methods have been developed to predict classical heptads using manually annotated coiled-coil domains. In this paper we focus on the prediction structurally-determined coiled-coil segments. We introduce a new method based on hidden Markov models that complement the existing methods and outperforms them in the task of locating structurallydefined coiled-coil segments.
International audienceIn this paper I shall adopt a possible reading of the notions of ‘explanatory indispensability’ and ‘genuine mathematical explanation in science’ on which the Enhanced Indispensability Argument (EIA) proposed by Alan Baker is based. Furthermore, I shall propose two examples of mathematical explanation in science and I shall show that, whether the EIA-partisans accept the reading I suggest, they are easily caught in a dilemma. To escape this dilemma they need to adopt some account of explanation and offer a plausible answer to the following ‘question of evidence’: What is a genuine mathematical explanation in empirical science and on what basis do we consider it as such? Finally, I shall suggest how a possible answer to the question of evidence might be given through a specific account of mathematical explanation in science. Nevertheless, the price of adopting this standpoint is that the genuineness of mathematical explanations of scientific facts turns out to be dependent on pragmatic constraints and therefore cannot be plugged in EIA and used to establish existential claims about mathematical objects
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