A stochastic evolutionary model for protein structure alignment and phylogeny.
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ABSTRACT:
SUBMITTER: Challis CJ
PROVIDER: S-EPMC3697813 | biostudies-literature | 2012 Nov
REPOSITORIES: biostudies-literature
Publications
A stochastic evolutionary model for protein structure alignment and phylogeny.
Challis Christopher J CJ Schmidler Scott C SC
Molecular biology and evolution 20120621 11
We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully acc ...[more]
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