Titlebook: Computational Methods in Protein Evolution; Tobias Sikosek Book 2019 Springer Science+Business Media, LLC, part of Springer Nature 2019 ph

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Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptatiring properties of extant proteins. As an illustrative example, we describe the protocol for the rapid identification of hotspots determining the binding of the two subunits within the heteromeric complex imidazole glycerol phosphate synthase.

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Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information,g how the inclusion of structural information can be used to inform joint estimation of alignments and trees. StructAlign can also be used to infer branch-specific rates of structural evolution, and analysis of an example globin dataset highlights strong variation in the inferred rate across the tre

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The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference,sites approximation that can be readily incorporated in maximum likelihood methods of phylogenetic inference, including ancestral sequence reconstruction. Next, we describe its validation with simulated and real proteins and its limitations and advantages with respect to empirical models that lack s

CEDE

Navigating Among Known Structures in Protein Space, The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole

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Interface-Based Structural Prediction of Novel Host-Pathogen Interactions,ed for efficient and robust computational approaches to predict HPIs and their complex (bound) structures. In this chapter, we review the first and currently only interface-based computational approach to identify novel HPIs. The concept of interface mimicry promises to identify more HPIs than compl

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Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function,