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This volume details computational tools for the study of protein evolution based on 1D-sequence and 3D-structure databases. Chapters guide readers through the analysis of 1D protein sequences for coevolutionary fold prediction, protein-nucleic acid interactions, distant homologs and functional motifs, characterization of fold energetics, disordered proteins, mutagenesis-driven modulation of conformational landscapes, 3D protein domains, prediction of 3D protein-protein interactions, and hybrid methods that mine both 1D and 3D genomic and protein databases for gene editing and alternative splicing. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Protein Evolution: Methods and Protocols aims to be comprehensive guide for researchers in the field.
List of contents
Distant Homology BLASTP Searches identify Neuropeptide Counterparts across Species.- Predicting Protein Folding Dynamics using Sequence Information.- Predictive Model for Single-site Mutations that change Intrinsically Disordered Protein Binding Energetics.- Detection of Specificity-determining Positions in Protein Families.- Co-Var, a measure to determine intra-protein, inter-protein, protein-DNA or protein-RNA co-evolution.- adabmDCA 2.0 A flexible but easy-to-use package for direct coupling analysis.- Unlocking Protein Evolution Insights: Efficient and Interpretable Mutational Effect Predictions with GEMME.- Using Total Network Dissimilarity to Analyze Protein Structures across Homologs.- Allosteric Network Analysis Toolkit for Single-Domain PhosphoProteins.- Computational identification of potential shape-shifting proteins from structures.- Transition state-based computational enzyme design.- Quantification of conformational changes of kinase regulators, kinases and regulator - kinase complexes using the TSR algorithm.- Identifying functional Water Encapsulation Sites within the Transmembrane Domain of Sensor Kinases.- Protein-Protein Interaction Site Prediction via EquiPPIS and its Application in Studying Viral Replication.- Modeling protein-protein complexes by combining pyDock and AlphaFold.- Binding affinity prediction of membrane protein-protein complexes using MPA-Pred.- Computational Methods to Engineer Cas Proteins for Efficient Genome Editing.- Exploring the Functional Consequences of Protein-Coding Alternative Splice Variants at a Genome scale: A Guide to Utilizing Expansion.
Summary
This volume details computational tools for the study of protein evolution based on 1D-sequence and 3D-structure databases. Chapters guide readers through the analysis of 1D protein sequences for coevolutionary fold prediction, protein-nucleic acid interactions, distant homologs and functional motifs, characterization of fold energetics, disordered proteins, mutagenesis-driven modulation of conformational landscapes, 3D protein domains, prediction of 3D protein-protein interactions, and hybrid methods that mine both 1D and 3D genomic and protein databases for gene editing and alternative splicing. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions tothe material, lists of necessary materials and reagents, step-by-step, readilyreproducible laboratory protocols, and a Notes section which highlightstips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Protein Evolution: Methods and Protocols aims to be comprehensive guide forresearchers in the field.
