Computational Methods in Protein Evolution

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