![]() ![]() The latter is, for instance, the case in the calcium-binding sites of calmodulin, which has 360 close homologs in the PDB.Ĭomparing the models while avoiding the superposition step, which implicitly requires many choices as to the type of superposition algorithm and its parameters (for example, when considering how to compare a multi-domain protein with relative domain movement), has advantages (Nicholls et al., 2014 ). Furthermore, differences are easily overlooked or difficult to assess in a visual inspection by means of superposition, especially if they are subtle or involve large (local) changes that make alignment particularly challenging or if there is a very large set of homologs available for inspection. Effective comparison typically allows only a few structure models before the view becomes too crowded to be informative. Structure models are compared by structural superposition, which can be performed by a large repertoire of algorithms that place emphasis on different features of the structure models. ![]() It is difficult to visualize such a wealth of data efficiently. As of June 2019, the median number of homologous protein chains with a sequence identity of 70% is 28, while the average is 145. ![]() The Protein Data Bank (PDB Bernstein et al., 1977 Burley et al., 2019 ) contains an ever-increasing wealth of homologous structural data. ![]()
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