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Abstract Details

Activity Number: 289
Type: Topic Contributed
Date/Time: Tuesday, July 31, 2012 : 8:30 AM to 10:20 AM
Sponsor: Section on Bayesian Statistical Science
Abstract - #305330
Title: A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny
Author(s): Christopher Challis*+ and Scott Schmidler
Companies: Duke University and Duke University
Address: Duke University, Durham, NC, 27708, United States
Keywords: Bayesian ; phylogeny ; protein structure ; alignment ; evolution

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, while 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 accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution.

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