Computational Methods in Protein Evolution, 1st ed. 2019 Methods in Molecular Biology Series, Vol. 1851

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.

Preface...

Table of Contents...

Contributing Authors...

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

Alexey Strokach, Carles Corbi-Verge, Joan Teyra, and Philip M. Kim

Matteo Aldeghi, Bert L. de Groot, and Vytautas Gapsys 

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

Laurel R. Yohe, Liang Liu, Liliana M. Dávalos, and David A. Liberles

Nikolaos Vakirlis and Aoife McLysaght

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

Ricardo Nascimento dos Santos, Xianli Jiang, Leandro Martínez, and Faruck Morcos

Mariano Avino and Art F.Y. Poon

7. Context-Dependent Mutation Effects in Proteins

Frank J. Poelwijk

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

Kelsey Aadland, Charles Pugh, and Bryan Kolaczkowski

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

Kristina Heyn and Rainer Merkl

10. Enhancing Statistical Multiple Sequence Alignment and Tree Inference using Structural Information

Joseph L. Herman

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

Ugo Bastolla and Miguel Arenas

12. Navigating Among Known Structures in Protein Space

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

Jonathan N. Wells and Joseph A. Marsh

14. Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function Jonathan D. Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M. Orengo, and Janet M. Thornton

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

Dustin Schaeffer and Nick V. Grishin

16. A Roadmap to Domain Based Proteomics

Carsten Kemena and Erich Bornberg-Bauer

17. Modelling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information

Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Andrew Waterhouse, Martino Bertoni, Lorenza Bordoli, Torsten Schwede, and Rosalba Lepore

18. Interface-Based Structural Prediction of Novel Host-Pathogen Interactions Emine Guven-Maiorov, Chung-Jung Tsai, Buyong Ma, and Ruth Nussinov

19. Predicting Functions of Disordered Proteins with MoRFpred

Christopher Oldfield, Vladimir N. Uversky, and Lukasz Kurgan

20. Exploring Protein Conformational Diversity

Alexander Miguel Monzon, Maria Silvina Fornasari, Diego Javier Zea, and Gustavo Parisi

21. High-Throughput Antibody Structure Modelling and Design using ABodyBuilder Jinwoo Leem and Charlotte M. Deane

22. In Silico Directed Evolution using CADEE

Beat Anton Amrein, Ashish Runthala, and Shina Caroline Lynn Kamerlin

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts