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Computer Simulations of Aggregation of Proteins and Peptides

  • Book
  • © 2022

Overview

Editors:
  1. Mai Suan Li

    1. Division of Theoretical Physics, Polish Academy of Sciences, Warsaw, Poland

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  2. Andrzej Kloczkowski

    1. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, USA

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  3. Marek Cieplak

    1. Instutute of Physics, Polish Academy of Sciences, Warsaw, Poland

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  4. Maksim Kouza

    1. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2340)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

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

    • Małgorzata Kotulska, Jakub W. Wojciechowski
    Pages 1-15

  3. Protocols for Rational Design of Protein Solubility and Aggregation Properties Using Aggrescan3D Standalone

    • Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
    Pages 17-40

  4. 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, Andrzej Kloczkowski
    Pages 41-50

  5. Computational Models for the Study of Protein Aggregation

    • Nguyen Truong Co, Mai Suan Li, Pawel Krupa
    Pages 51-78

  6. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field

    • Ana V. Rojas, Gia G. Maisuradze, Harold A. Scheraga, Adam Liwo
    Pages 79-104

  7. Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins

    • Marek Cieplak, Łukasz Mioduszewski, Mateusz Chwastyk
    Pages 105-120

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

    • Yifat Miller
    Pages 121-137

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

    • Orkid Coskuner-Weber, M. Gokhan Habiboglu, David Teplow, Vladimir N. Uversky
    Pages 139-173

  10. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

    • Phuong H. Nguyen, Philippe Derreumaux
    Pages 175-196

  11. All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

    • Satoru G. Itoh, Hisashi Okumura
    Pages 197-220

  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

    • Anna V. Glyakina, Nikolai K. Balabaev, Oxana V. Galzitskaya
    Pages 221-233

  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, Martin Carballo-Pacheco, Arghadwip Paul, Bogdan Barz et al.
    Pages 235-279

  14. Challenges in Experimental Methods

    • Marlena E. Gąsior-Głogowska, Natalia Szulc, Monika Szefczyk
    Pages 281-307

  15. Aggregates Sealed by Ions

    • Giovanni La Penna, Silvia Morante
    Pages 309-341

  16. Modifying Amyloid Motif Aggregation Through Local Structure

    • Sofia Bali, Lukasz A. Joachimiak
    Pages 343-356

  17. Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations

    • Rodrigo A. Moreira, Joseph L. Baker, Horacio V. Guzman, Adolfo B. Poma
    Pages 357-378

  18. Predictive Modeling of Neurotoxic α-Synuclein Polymorphs

    • Liang Xu, Shayon Bhattacharya, Damien Thompson
    Pages 379-399

  19. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace

    • Shayon Bhattacharya, Liang Xu, Damien Thompson
    Pages 401-448

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

    • Saba Shahzadi, Muhammad Yasir, Bisma Aftab, Sumbal Babar, Mubashir Hassan
    Pages 449-467
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Keywords

About this book

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.

Editors and Affiliations

  • Division of Theoretical Physics, Polish Academy of Sciences, Warsaw, Poland

    Mai Suan Li

  • Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, USA

    Andrzej Kloczkowski, Maksim Kouza

  • Instutute of Physics, Polish Academy of Sciences, Warsaw, Poland

    Marek Cieplak

Bibliographic Information

  • Book Title: Computer Simulations of Aggregation of Proteins and Peptides

  • Editors: Mai Suan Li, Andrzej Kloczkowski, Marek Cieplak, Maksim Kouza

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1546-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1545-4Published: 16 February 2022

  • Softcover ISBN: 978-1-0716-1548-5Published: 16 February 2022

  • eBook ISBN: 978-1-0716-1546-1Published: 15 February 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 478

  • Number of Illustrations: 7 b/w illustrations, 150 illustrations in colour

  • Topics: Protein Science, Bioinformatics

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