Computer Simulations of Aggregation of Proteins and Peptides

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. Application to the Interactions of E-cadherins.- Computational Models for 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 Neurodegenerative Diseases.- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.- All-atom Molecular Dynamics Simulation Methods for Aggregation of Protein and Peptides: Replica-exchange/permutationand Nonequilibrium Simulations.- Key Factors Controlling Fibril Formation of Proteins- Determination of the Most Stable Packing Of Peptides From Ribosomal S1 Protein, Protein Bgl2p and Aβ peptide in β-layers during Molecular Dynamics Simulations.- Molecular Dynamics Simulations Of Protein Aggregation: Protocols For Simulation Setup and Analysis with Markov State Models And Transition Networks.- 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.- Computational Studies of Protein Aggregation In Preeclampsia.- Final remarks.