Directionality in protein fold prediction |
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Authors: | Jonathan J Ellis Fabien PE Huard Charlotte M Deane Sheenal Srivastava Graham R Wood |
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Institution: | (1) Department of Statistics, Macquarie University, Sydney, NSW, 2109, Australia;(2) Department of Statistics, Oxford University, 1 South Parks Road, Oxford, OX1 3TG, UK |
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Abstract: | Background Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state,
it has been frequently stated by the protein fold prediction community that all the information required for protein folding
lies in the amino acid sequence. Recent in vitro experiments and in silico computational studies, however, have shown that
cotranslation may affect the folding pathway of some proteins, especially those of ancient folds. In this paper aspects of
cotranslational folding have been incorporated into a protein structure prediction algorithm by adapting the Rosetta program
to fold proteins as the nascent chain elongates. This makes it possible to conduct a pairwise comparison of folding accuracy,
by comparing folds created sequentially from each end of the protein. |
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