Computational Methods in Protein Evolution

Predicting the Effect of Mutations on Protein Folding and Protein-Protein Interactions.- Accurate Calculation of Free Energy Changes Upon Amino Acid Mutation.- Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates.- Computational Prediction of De Novo Emerged Protein-Coding Genes.- Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations.- Detecting Amino Acid Coevolution with Bayesian Graphical Models.- Context-Dependent Mutation Effects in Proteins.- High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function.- Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation.- Enhancing Statistical Multiple Sequence Alignment and Tree Inference using Structural Information.- The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference.- Navigating Among Known Structures in Protein Space.- A Graph-Based Approach for Detecting Sequence Homology in Highly Diverged Repeat-Protein Families.- Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.- Identification of Protein Homologs and Domain Boundaries by Iterative Sequence Alignment.- A Roadmap to Domain Based Proteomics.- Modelling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information.- Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.- Predicting Functions of Disordered Proteins with MoRFpred.- Exploring Protein Conformational Diversity.- High-Throughput Antibody Structure Modelling and Design using ABodyBuilder.- In Silico Directed Evolution using CADEE.