Computational Peptide Science: Methods and Protocols

ISBN-13: 9781071618578 / Angielski

Thomas Simonson

Opis

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.

Spis treści

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 β-strand Sequences

Yoonjoo Choi

 

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

Phuong Hoang Nguyen, Pierre Tufféry, 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 Tˆap 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. Röhrig, 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