Simonson Thomas (ed.) Computational Peptide Science. Methods and Protocols

Springer Science+Business Media, 2022. — 427 p. — (Methods in Molecular Biology 2405). — ISBN 978-1-0716-1854-7; ISBN 978-1-0716-1855-4.For over 35 years, biological scientists have come to rely on the research protocols and methodologies in the critically acclaimed Methods in Molecular Biology series. The series was the first to introduce the step-by-step protocols approach that has become the standard in all biomedical protocol publishing. Each protocol is provided in readily-reproducible step-bystep fashion, opening with an introductory overview, a list of the materials and reagents needed to complete the experiment, and followed by a detailed procedure that is supported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitute the key ingredient in each and every volume of the Methods in Molecular Biology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexed in PubMed.Preface
Contributors
Machine Learning Prediction of Antimicrobial Peptides
Guangshun Wang, Iosif I. Vaisman, and Monique L. van Hoek
Tools for Characterizing Proteins: Circular Variance, Mutual Proximity, Chameleon Sequences, and Subsequence Propensities
Mihaly Mezei
Exploring the Peptide Potential of Genomes
Chris Papadopoulos, Nicolas Chevrollier, and Anne Lopes
Computational Identification and Design of Complementary β-Strand Sequences
Yoonjoo Choi
Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations
Phuong Hoang Nguyen, Pierre Tuffe´ry, and Philippe Derreumaux
Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes
Charles H. Chen, Karen Pepper, Jakob P. Ulmschneider, Martin B. Ulmschneider, and Timothy K. Lu
Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides
Manuel N. Melo
Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions
Joseph Clayton, Lokesh Baweja, and Jeff Wereszczynski
Metadynamics Simulations to Study the Structural Ensembles and Binding Processes of Intrinsically Disordered Proteins
Rui Zhou and Mojie Duan
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
Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions
Maxence Delaunay and Taˆp Ha-Duong
Rapid Rational Design of Cyclic Peptides Mimicking Protein–Protein Interfaces
Brianda L. Santini and Martin Zacharias
Structural Prediction of Peptide–MHC Binding Modes
Marta A. S. Perez, Michel A. Cuendet, Ute F. Ro¨hrig, Olivier Michielin, and Vincent Zoete
Molecular Simulation of Stapled Peptides
Victor Ovchinnikov, Aravinda Munasinghe, and Martin Karplus
Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria
Emilio Gallicchio
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
Computational Design of Miniprotein Binders
Younes Bouchiba, Manon Ruffini, Thomas Schiex, and Sophie Barbe
Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain
Eleni Michael, Savvas Polydorides, and Georgios Archontis
Knowledge-Based Unfolded State Model for Protein Design
Vaitea Opuu, David Mignon, and Thomas Simonson
Index