Computational Methods in Protein Evolution

Preface...Table of Contents...Contributing Authors...1.Predicting the Effect of Mutations on Protein Folding and Protein-Protein InteractionsAlexey Strokach, Carles Corbi-Verge, Joan Teyra, and Philip M. Kim2.Accurate Calculation of Free Energy Changes Upon Amino Acid MutationMatteo Aldeghi, Bert L. de Groot, and Vytautas Gapsys 3.Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene DuplicatesLaurel R. Yohe, Liang Liu, Liliana M. Dávalos, and David A. Liberles4.Computational Prediction of De Novo Emerged Protein-Coding GenesNikolaos Vakirlis and Aoife McLysaght5.Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native ConformationsRicardo Nascimento dos Santos, Xianli Jiang, Leandro Martínez, and Faruck Morcos6.Detecting Amino Acid Coevolution with Bayesian Graphical ModelsMariano Avino and Art F.Y. Poon7.Context-Dependent Mutation Effects in ProteinsFrank J. Poelwijk8.High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular FunctionKelsey Aadland, Charles Pugh, and Bryan Kolaczkowski9.Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary AdaptationKristina Heyn and Rainer Merkl10.Enhancing Statistical Multiple Sequence Alignment and Tree Inference using Structural InformationJoseph L. Herman11.The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic InferenceUgo Bastolla and Miguel Arenas12.Navigating Among Known Structures in Protein SpaceAya Narunsky, Nir Ben-Tal, and Rachel Kolodny13.A Graph-Based Approach for Detecting Sequence Homology in Highly Diverged Repeat-Protein FamiliesJonathan N. Wells and Joseph A. Marsh14.Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function Jonathan D. Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M. Orengo, and Janet M. Thornton15.Identification of Protein Homologs and Domain Boundaries by Iterative Sequence AlignmentDustin Schaeffer and Nick V. Grishin16.A Roadmap to Domain Based ProteomicsCarsten Kemena and Erich Bornberg-Bauer17.Modelling of Protein Tertiary and Quaternary Structures Based on Evolutionary InformationGabriel Studer, Gerardo Tauriello, Stefan Bienert, Andrew Waterhouse, Martino Bertoni, Lorenza Bordoli, Torsten Schwede, and Rosalba Lepore18.Interface-Based Structural Prediction of Novel Host-Pathogen Interactions Emine Guven-Maiorov, Chung-Jung Tsai, Buyong Ma, and Ruth Nussinov19.Predicting Functions of Disordered Proteins with MoRFpredChristopher Oldfield, Vladimir N. Uversky, and Lukasz Kurgan20.Exploring Protein Conformational DiversityAlexander Miguel Monzon, Maria Silvina Fornasari, Diego Javier Zea, and Gustavo Parisi21.High-Throughput Antibody Structure Modelling and Design using ABodyBuilder Jinwoo Leem and Charlotte M. Deane22.In Silico Directed Evolution using CADEEBeat Anton Amrein, Ashish Runthala, and Shina Caroline Lynn Kamerlin... Mehr