Textbook in PDF format

This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer’s, Parkinson’s, and preeclampsia. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.
Preface
Contributors
Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins
Protocols for Rational Design of Protein Solubility and Aggregation Properties Using Aggrescan3D Standalone
Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Applicat...
Computational Models for the Study of Protein Aggregation
Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field
Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins
Molecular Insights into the Effect of Metals on Amyloid Aggregation
From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenera...
Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation
All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permu...
Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β...
Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov Sta...
Challenges in Experimental Methods
Aggregates Sealed by Ions
Modifying Amyloid Motif Aggregation Through Local Structure
Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations
Predictive Modeling of Neurotoxic α-Synuclein Polymorphs
Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace
Exploration of Protein Aggregations in Parkinson´s Disease Through Computational Approaches and Big Data Analytics
Final Remarks
Index