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Computational Peptide Science

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Thomas Simonson

    1. Lab de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France

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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 2405)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Machine Learning Prediction of Antimicrobial Peptides

    • Guangshun Wang, Iosif I. Vaisman, Monique L. van Hoek
    Pages 1-37

  3. Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities

    • Mihaly Mezei
    Pages 39-61

  4. Exploring the Peptide Potential of Genomes

    • Chris Papadopoulos, Nicolas Chevrollier, Anne Lopes
    Pages 63-82

  5. Computational Identification and Design of Complementary β-Strand Sequences

    • Yoonjoo Choi
    Pages 83-94

  6. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations

    • Phuong Hoang Nguyen, Pierre Tufféry, Philippe Derreumaux
    Pages 95-113

  7. Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes

    • Charles H. Chen, Karen Pepper, Jakob P. Ulmschneider, Martin B. Ulmschneider, Timothy K. Lu
    Pages 115-136

  8. Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides

    • Manuel N. Melo
    Pages 137-150

  9. Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions

    • Joseph Clayton, Lokesh Baweja, Jeff Wereszczynski
    Pages 151-167

  10. Metadynamics Simulations to Study the Structural Ensembles and Binding Processes of Intrinsically Disordered Proteins

    • Rui Zhou, Mojie Duan
    Pages 169-178

  11. Computational and Experimental Protocols to Study Cyclo-dihistidine Self- and Co-assembly: Minimalistic Bio-assemblies with Enhanced Fluorescence and Drug Encapsulation Properties

    • Asuka A. Orr, Yu Chen, Ehud Gazit, Phanourios Tamamis
    Pages 179-203

  12. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions

    • Maxence Delaunay, Tâp Ha-Duong
    Pages 205-230

  13. Rapid Rational Design of Cyclic Peptides Mimicking Protein–Protein Interfaces

    • Brianda L. Santini, Martin Zacharias
    Pages 231-244

  14. Structural Prediction of Peptide–MHC Binding Modes

    • Marta A. S. Perez, Michel A. Cuendet, Ute F. Röhrig, Olivier Michielin, Vincent Zoete
    Pages 245-282

  15. Molecular Simulation of Stapled Peptides

    • Victor Ovchinnikov, Aravinda Munasinghe, Martin Karplus
    Pages 283-301

  16. Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria

    • Emilio Gallicchio
    Pages 303-334

  17. Computational Evolution Protocol for Peptide Design

    • Rodrigo Ochoa, Miguel A. Soler, Ivan Gladich, Anna Battisti, Nikola Minovski, Alex Rodriguez et al.
    Pages 335-359

  18. Computational Design of Miniprotein Binders

    • Younes Bouchiba, Manon Ruffini, Thomas Schiex, Sophie Barbe
    Pages 361-382

  19. Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain

    • Eleni Michael, Savvas Polydorides, Georgios Archontis
    Pages 383-402

  20. Knowledge-Based Unfolded State Model for Protein Design

    • Vaitea Opuu, David Mignon, Thomas Simonson
    Pages 403-424
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Keywords

About this book

This volume details current and new computational methodologies to study peptides.  Chapters guide readers through antimicrobial peptides, foldability, amyloid sheet formation, membrane-active peptides, organized peptide assemblies, protein-peptide interfaces, prediction of peptide-MHC complexes, advanced free energy simulations for peptide binding, and methods for high throughput peptide or miniprotein design. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, software, and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

 

Authoritative and cutting-edge, Computational Peptides Science: Methods and Protocols aims to provide concepts, methods, and guidelines to help both novices and experienced workers benefit from today's new opportunities and challenges.


Editors and Affiliations

  • Lab de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France

    Thomas Simonson

Bibliographic Information

  • Book Title: Computational Peptide Science

  • Book Subtitle: Methods and Protocols

  • Editors: Thomas Simonson

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1855-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1854-7Published: 18 March 2022

  • Softcover ISBN: 978-1-0716-1857-8Published: 19 March 2023

  • eBook ISBN: 978-1-0716-1855-4Published: 17 March 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 427

  • Number of Illustrations: 10 b/w illustrations, 83 illustrations in colour

  • Topics: Bioinformatics, Life Sciences, general

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