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Computational Methods in Protein Evolution

  • Tobias Sikosek

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

Table of contents

  1. Front Matter
    Pages i-xiii
  2. Alexey Strokach, Carles Corbi-Verge, Joan Teyra, Philip M. Kim
    Pages 1-17
  3. Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
    Pages 19-47
  4. Laurel R. Yohe, Liang Liu, Liliana M. Dávalos, David A. Liberles
    Pages 49-62
  5. Nikolaos Vakirlis, Aoife McLysaght
    Pages 63-81
  6. Ricardo Nascimento dos Santos, Xianli Jiang, Leandro Martínez, Faruck Morcos
    Pages 83-103
  7. Mariano Avino, Art F. Y. Poon
    Pages 105-122
  8. Frank J. Poelwijk
    Pages 123-134
  9. Kelsey Aadland, Charles Pugh, Bryan Kolaczkowski
    Pages 135-170
  10. Aya Narunsky, Nir Ben-Tal, Rachel Kolodny
    Pages 233-249
  11. Jonathan D. Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M. Orengo, Janet M. Thornton
    Pages 263-275
  12. Carsten Kemena, Erich Bornberg-Bauer
    Pages 287-300
  13. Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Andrew Mark Waterhouse, Martino Bertoni, Lorenza Bordoli et al.
    Pages 301-316
  14. Emine Guven-Maiorov, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov
    Pages 317-335
  15. Christopher J. Oldfield, Vladimir N. Uversky, Lukasz Kurgan
    Pages 337-352
  16. Alexander Miguel Monzon, Maria Silvina Fornasari, Diego Javier Zea, Gustavo Parisi
    Pages 353-365
  17. Beat Anton Amrein, Ashish Runthala, Shina Caroline Lynn Kamerlin
    Pages 381-415
  18. Back Matter
    Pages 417-420

About this book

Introduction

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.

Keywords

phylogenetic trees sequence reconstruction co-evolution Epistasis allostery

Editors and affiliations

  • Tobias Sikosek
    • 1
  1. 1.GlaxoSmithKlineCellzome – a GSK company Meyerhofstrasse 1HeidelbergGermany

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-4939-8736-8
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-8735-1
  • Online ISBN 978-1-4939-8736-8
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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