11/18/2023 0 Comments Ncbi nucleotideFinally we tested the reliability of our method in a real world case in which it has to predict nucleotide-binding sites in unbound proteins. We calculated that in the 59% of the analyzed proteins the method ranks as first a reconstructed binding site or a part of it. Furthermore we attempted to reconstruct the full structure of the binding site, starting from the predicted positions of the fragments. The method is able to rank as first a correct prediction in the 48%, 48% and 68% of the analyzed proteins for the nucleobase, carbohydrate and phosphate respectively, while considering the first five predictions the performances change to 71%, 65% and 86% respectively. Predictions falling inside the surface of the protein are discarded, and the remaining ones are scored using clustering and conservation. Whenever a similarity is found the fragment bound by the template is transferred on the query protein, thus identifying a putative binding site. Our method predicts binding sites for each nucleotide fragment by comparing a query protein with a database of templates extracted from proteins of known structure. Moreover these motifs behave as modules and are found in different combinations across fold space. These fragments are bound by specific structural motifs that recur in proteins of different fold. the phosphate, the nucleobase and the carbohydrate moieties. Nucleotides are composed of identifiable fragments, i.e. Here we propose a novel methodology that leverages the observation that nucleotide-binding sites have a modular structure. Both sequence and structure based methods have been developed to predict the location of nucleotide-binding sites in proteins. Nucleotides are involved in several cellular processes, ranging from the transmission of genetic information, to energy transfer and storage.
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