Download A Bayes-optimal sequence-structure theory that unifies by Lathrop R. H., Rogers Jr R. G., Smith T. F. PDF

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 series, specific formulae are derived to choose (1) its globally such a lot possible middle constitution from a constitution library; (2) its globally so much possible alignment to a given middle constitution; (3) its such a lot possible joint middle constitution and alignment selected globally around the whole library; and (4) its such a lot possible person segments, secondary constitution, and super-secondary buildings around the whole library. The computations concerned are NP-hard within the normal case (3D-3D). speedy certain recursions for the limited series singleton-only (1D-3D) case are given. Conclusions comprise: (a) the main possible joint center constitution and alignment isn't inevitably the main possible alignment of the main possible center constitution, yet quite maximizes the manufactured from center and alignment chances; (b) use of a sequence-independent linear or affine hole penalty can result within the highest-probability threading no longer having the bottom rating; (c) determining the main possible center constitution from the library (core constitution choice or fold popularity basically) consists of evaluating percentages summed over all attainable alignments of the series to the middle, and never evaluating person optimum (or near-optimal) sequence-structure alignments; and (d) assuming uninformative priors, middle constitution choice is resembling evaluating the ratio of 2 worldwide capability.

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Additional info for A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment

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Principles of protein folding - a perspective from simple exact models. Protein Science 4, 561-602. Dunbrack Jr, R. L. and F. E. Cohen (1997). Bayesian statistical analysis of protein sidechain rotamer preferences, Protein Science 6, 166 l-l 68 1. Fetrow, J. S. and S. H. Bryant (1993). New programs for protein tertiary structure prediction. Bio/Technology 11, 479-484. , A. Y. Badretdinov and A. M. Gutin (1995). Why do proteins have Boltzmann-like statistics? Proteins: Structure, Function, and Genetics 23, 142-150.

255, 641-665. Lawrence, C. , S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald and J. C. Wootton (1993). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262, 208214. Lemer, C. , M. J. Rooman and S. J. Wodak (1995). Protein structure prediction by threading methods: Evaluation of current techniques. Proteins: Structure, Function, and Genetics 23 337-355. , J. U, Bowie and D. Eisenberg (1992). Assessment of protein models with three-dimensional profiles.

L. Lo Conte, J. Bienkowska, C. Gaitatzes, R. G. Rogers Jr and R. H. Lathrop (1997). Current limitations to protein threading approaches. J. Camp. Biol. 4, 2 17-225. Srinivasan, R. and G. D. Rose (1995). LINUS: A hierarchic procedure to predict the fold of a protein. Proteins: Structure, Function, and Genetics 22, 81-99. Stultz, C. , R. Nambudripad, R. H. Lathrop and J. V. White (1995) Predicting protein structure with probabilistic models, in Protein Folding and Stability, N. Allewell and C. Woodward (Eds), Greenwich: JAI Press, in press.

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