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Computational Methods in Protein Evolution

  • Book
  • © 2019

Overview

Editors:
  1. Tobias Sikosek

    1. GlaxoSmithKline, Cellzome – a GSK company Meyerhofstrasse 1, Heidelberg, Germany

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1851)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Predicting the Effect of Mutations on Protein Folding and Protein-Protein Interactions

    • Alexey Strokach, Carles Corbi-Verge, Joan Teyra, Philip M. Kim
    Pages 1-17

  3. Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

    • Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
    Pages 19-47

  4. Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates

    • Laurel R. Yohe, Liang Liu, Liliana M. Dávalos, David A. Liberles
    Pages 49-62

  5. Computational Prediction of De Novo Emerged Protein-Coding Genes

    • Nikolaos Vakirlis, Aoife McLysaght
    Pages 63-81

  6. Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations

    • Ricardo Nascimento dos Santos, Xianli Jiang, Leandro Martínez, Faruck Morcos
    Pages 83-103

  7. Detecting Amino Acid Coevolution with Bayesian Graphical Models

    • Mariano Avino, Art F. Y. Poon
    Pages 105-122

  8. Context-Dependent Mutation Effects in Proteins

    • Frank J. Poelwijk
    Pages 123-134

  9. High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function

    • Kelsey Aadland, Charles Pugh, Bryan Kolaczkowski
    Pages 135-170

  10. Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation

    • Kristina Straub, Rainer Merkl
    Pages 171-182

  11. Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information

    • Joseph L. Herman
    Pages 183-214

  12. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference

    • Ugo Bastolla, Miguel Arenas
    Pages 215-231

  13. Navigating Among Known Structures in Protein Space

    • Aya Narunsky, Nir Ben-Tal, Rachel Kolodny
    Pages 233-249

  14. A Graph-Based Approach for Detecting Sequence Homology in Highly Diverged Repeat Protein Families

    • Jonathan N. Wells, Joseph A. Marsh
    Pages 251-261

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

    • Jonathan D. Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M. Orengo, Janet M. Thornton
    Pages 263-275

  16. Identification of Protein Homologs and Domain Boundaries by Iterative Sequence Alignment

    • Dustin Schaeffer, Nick V. Grishin
    Pages 277-286

  17. A Roadmap to Domain Based Proteomics

    • Carsten Kemena, Erich Bornberg-Bauer
    Pages 287-300

  18. Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information

    • Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Andrew Mark Waterhouse, Martino Bertoni, Lorenza Bordoli et al.
    Pages 301-316

  19. Interface-Based Structural Prediction of Novel Host-Pathogen Interactions

    • Emine Guven-Maiorov, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov
    Pages 317-335

  20. Predicting Functions of Disordered Proteins with MoRFpred

    • Christopher J. Oldfield, Vladimir N. Uversky, Lukasz Kurgan
    Pages 337-352
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Keywords

About this book

This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.



Editors and Affiliations

  • GlaxoSmithKline, Cellzome – a GSK company Meyerhofstrasse 1, Heidelberg, Germany

    Tobias Sikosek

Bibliographic Information

  • Book Title: Computational Methods in Protein Evolution

  • Editors: Tobias Sikosek

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8736-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-8735-1Published: 09 October 2018

  • Softcover ISBN: 978-1-4939-9378-9Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8736-8Published: 08 October 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 420

  • Number of Illustrations: 23 b/w illustrations, 80 illustrations in colour

  • Topics: Protein Science

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