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By Lathrop R. H., Rogers Jr R. G., Smith T. F.

A rigorous Bayesian research is gifted that unifies protein sequence-structure alignment and popularity. Given a chain, specific formulae are derived to choose (1) its globally such a lot possible middle constitution from a constitution library; (2) its globally such a lot possible alignment to a given middle constitution; (3) its so much possible joint center constitution and alignment selected globally around the whole library; and (4) its such a lot possible person segments, secondary constitution, and super-secondary constructions around the whole library. The computations concerned are NP-hard within the basic case (3D-3D). speedy particular recursions for the limited series singleton-only (1D-3D) case are given. Conclusions contain: (a) the main possible joint center constitution and alignment isn't really inevitably the main possible alignment of the main possible center constitution, yet particularly maximizes the manufactured from center and alignment percentages; (b) use of a sequence-independent linear or affine hole penalty can result within the highest-probability threading no longer having the bottom ranking; (c) making a choice on the main possible center constitution from the library (core constitution choice or fold acceptance purely) consists of evaluating percentages summed over all attainable alignments of the series to the center, and never evaluating person optimum (or near-optimal) sequence-structure alignments; and (d) assuming uninformative priors, center constitution choice is similar to evaluating the ratio of 2 worldwide capacity.

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A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment by Lathrop R. H., Rogers Jr R. G., Smith T. F.


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