Computational methods in protein evolution
Author(s)
Bibliographic Information
Computational methods in protein evolution
（Methods in molecular biology / John M. Walker, series editor, 1851）（Springer protocols）
Humana Press, c2019
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
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
2. Accurate Calculation of Free Energy Changes Upon Amino Acid Mutation
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. Davalos, and David A. Liberles
4. Computational Prediction of De Novo Emerged Protein-Coding Genes
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 Martinez, and Faruck Morcos
6. Detecting Amino Acid Coevolution with Bayesian Graphical Models
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
Aya Narunsky, Nir Ben-Tal, and Rachel Kolodny
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
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