Computational peptide science : methods and protocols
Author(s)
Bibliographic Information
Computational peptide science : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2405）（Springer protocols）
Humana Press, c2022
- : [hardback]
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
1. Machine Learning Prediction of Antimicrobial Peptides
Guangshun Wang, Iosif I. Vaisman, and Monique L. van Hoek
2. Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences and Subsequence Propensities
Mihaly Mezei
3. Exploring the Peptide Potential Of Genomes
Chris Papadopoulos, Nicolas Chevrollier, and Anne Lopes
4. Computational Identification and Design of Complementary -strand Sequences
Yoonjoo Choi
5. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations
Phuong Hoang Nguyen, Pierre Tuffery, and Philippe Derreumaux
6. Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes
Charles H. Chen, Karen Pepper, Jakob P. Ulmschneider, Martin B. Ulmschneider, and Timothy K. Lu
7. Coarse-grain simulations of membrane-adsorbed helical peptides
Manuel N. Melo
8. Peptide dynamics and metadynamics: leveraging enhanced sampling molecular dynamics to robustly model long-timescale transitions
Joseph Clayton, Lokesh Baweja, and Jeff Wereszczynski
9. Metadynamics Simulations to Study the Structural Ensembles and Binding Processes of Intrinsically Disordered Proteins
Rui Zhou and Mojie Duan
10. 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, and Phanourios Tamamis
11. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions
Maxence Delaunay and Tap Ha-Duong
12. Rapid Rational Design of Cyclic Peptides Mimicking Protein-Protein Interfaces
Brianda L. Santini and Martin Zacharias
13. Structural prediction of peptide-MHC binding modes
Marta A.S. Perez, Michel A. Cuendet, Ute F. Roehrig, Olivier Michielin, and Vincent Zoete
14. Molecular Simulation of Stapled Peptides
Victor Ovchinnikov, Aravinda Munasinghe, and Martin Karplus
15. Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria
Emilio Gallicchio
16. Computational Evolution Protocol for Peptide Design
Rodrigo Ochoa, Miguel A. Soler, Ivan Gladich, Anna Battisti, Nikola Minovski, Alex Rodriguez, Sara Fortuna, Pilar Cossio, and Alessandro Laio
17. Computational design of miniprotein binders
Younes Bouchiba, Manon Ruffini, Thomas Schiex, and Sophie Barbe
18. Computational Design of LD Motif-Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain
Eleni Michael, Savvas Polydorides and Georgios Archontis
19. Knowledge-based unfolded state model for protein design
Vaitea Opuu, David Mignon and Thomas Simonson
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