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Prediction of protein structures continues to be a difficult problem, particularly when there are no solved structures for homologous proteins to use as templates. Local structure prediction (secondary structure and burial) is fairly reliable, but does not provide enough information to produce complete three-dimensional structures. Residue-residue contact… (More)

MOTIVATION
Hidden Markov models (HMMs) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases owing to sequence length and composition… (More)

Motivation: Hidden Markov models (hmms) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases due to sequence length and composition and… (More)

- George Shackelford, Kevin Karplus, Richard Hughey, Herbert Lee, Tyrus Miller
- 2010

x Dedication xii Acknowledgments xiii 1 Introduction 1 1.

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