Computer Simulations of Aggregation of Proteins and Peptides

1. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins

Malgorzata Kotulska and Jakub W. Wojciechowski

2. Protocols for Rational Design of Protein Solubility and Aggregation Properties using Aggrescan3D Standalone

Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Jordi Pujols, Salvador Ventura, and Sebastian Kmiecik

3. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites. Application to the Interactions of E-cadherins

Robert L. Jernigan, Pranav Khade, Ambuj Kumar, and Andrzej Kloczkowski

4. Computational Models for Study of Protein Aggregation

Nguyen Truong Co, Mai Suan Li, and Pawel Krupa

5. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field Ana V. Rojas, Gia G. Maisuradze, Harold A. Scheraga, and Adam Liwo

6. Contact-based Analysis of Aggregation of Intrinsically Disordered Proteins

Marek Cieplak, Lukasz Mioduszewski, and Mateusz Chwastyk

7. Molecular Insights into the Effect of Metals on Amyloid Aggregation

Yifat Miller

8. From Quantum Mechanics, Classical Mechanics and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases

Orkid Coskuner-Weber, M. Gokhan Habiboglu, David Teplow, and Vladimir N. Uversky

9. Computer Simulations Aimed at Exploring Protein Aggregation and
Dissociation

Phuong H. Nguyen and Philippe Derreumaux

10. All-atom Molecular Dynamics Simulation Methods for Aggregation of Protein and Peptides: Replica-exchange/permutation and Nonequilibrium Simulations

Satoru G. Itoh and Hisashi Okumura

11. Key Factors Controlling Fibril Formation of Proteins

Tran Thi Minh Thu, Andrzej Kloczkowski, Mai Suan Li, and Maksim Kouza

12. Determination of the Most Stable Packing Of Peptides From Ribosomal S1 Protein, Protein Bgl2p and Aβ
peptide in β
-layers during Molecular Dynamics Simulations

Glyakina A.V., Balabaev N.K., and Galzitskaya O.V

13. Molecular Dynamics Simulations Of Protein Aggregation: Protocols For Simulation Setup and Analysis with Markov State Models And Transition Networks

Suman Samantray, Wibke Schumann, Alexander-Maurice Illig, Arghadwip Paul, Bogdan Barz, and Birgit Strodel

14. Challenges in Experimental Methods

Marlena E. Gą
sior-Glogowska, Natalia Szulc, and Monika Szefczyk

15. Aggregates Sealed By Ions

Giovanni La Penna and Silvia Morante

16. Modifying Amyloid Motif Aggregation through Local Structure

Sofia Bali and Lukasz A. Joachimiak

17. Assessing the Stability Of Biological Fibrils By Molecular-Scale Simulations

Rodrigo A. Moreira

18. Predictive Modeling of Neurotoxic α
-Synuclein Polymorphs

Liang Xu, Shayon Bhattacharya, and Damien Thompson

19. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace

Shayon Bhattacharya, Liang Xu, and Damien Thompson

20. Exploration of Protein Aggregations in Parkinson's Disease through Computational Approaches and Big Data Analytics

Saba Shahzadi, Muhammad Yasir, Bisma Jawad, Sumbal Baber, Mubashir Hassan

21. Computational Studies of Protein Aggregation In Preeclampsia

Maksim Kouza, Andrzej Kolinski, Irina Buhimschi, and Andrzej Kloczkowski

22. Final remarks

Mai Suan Li, Andrzej Kloczkowski, Marek Cieplak, and Maks