Discriminative modelling of context-specific amino acid substitution probabilities

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HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

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Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds

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Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Context-specific amino acid substitution matrices and their use in the detection of protein homologs

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