Computational Methods in Protein Evolution (Hardcover, 2019)

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