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This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology modeling in the twilight zone and improving accuracy through sequence space analysis to approaches to construct multi-protein complex models, the book explores a wide variety of uses and applications of this valuable technique. Written for the highly successful Methods in Molecular Biology series, the chapters include introductions to their respective topics, lists of the necessary programs, webservers, and databases, step-by-step and readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Homology Modeling: Methods and Protocols serves as an ideal guide to recent homology modeling procedures, assumptions made, and model quality assessment that will illuminate the black box of homology modeling for novice readers and broaden the knowledge of this methodology for professionals.
Homology Modeling in the Twilight Zone:​ Improved Accuracy by Sequence Space Analysis
Illuminating the “Twilight Zone”:​ Advances in Difficult Protein Modeling
Contact-Assisted Threading in Low-Homology Protein Modeling
Omics and Remote Homology Integration to Decipher Protein Functionality
Easy Not Easy:​ Comparative Modeling with High-Sequence Identity Templates
Quality Estimates for 3D Protein Models
Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy
Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling
Homology Modeling of the G Protein-Coupled Receptors
Modeling of Olfactory Receptors
Analyses of Mutation Displacements from Homology Models
Persistent Homology for RNA Data Analysis
Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them
Homology Modeling of Transporter Proteins
Modeling of SARS-CoV-2 Virus Proteins:​ Implications on Its Proteome
Homology Modeling of Antibody Variable Regions:​ Methods and Applications
3D-BMPP:​ 3D Beta-Barrel Membrane Protein Predictor
Protein Homology Modeling for Effective Drug Design
Specificities of Protein Homology Modeling for Allosteric Drug Design
Modeling of Protein Complexes