Modeling and design of peptidomimetics to modulate protein-protein interactions / Andrew M. Watkins, Richard Bonneau, and Paramjit S. Arora. Detection of peptide-binding sites on protein surfaces using the peptimap server / Tanggis Bohnuud, George Jones, Ora Schueler-Furman, and Dima Kozakov -- Peptide suboptimal conformation sampling for the prediction of protein-peptide interactions / Alexis Lamiable, Pierre Thévenet, Stephanie Eustache, Adrien Saladin, Gautier Moroy, and Pierre Tuffery -- Template-based prediction of protein-peptide interactions by using GalaxyPepDock / Hasup Lee and Chaok Seok -- Application of the ATTRACT coarse-grained docking and atomistic refinement for predicting peptide-protein interactions / Christina Schindler and Martin Zacharias -- Highly flexible protein-peptide docking using CABS-Dock / Maciej Paweł Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, and Sebastian Kmiecik -- AnchorDock for blind flexible docking of peptides to proteins / Michal Slutzki, Avraham Ben-Shimon, and Masha Y. Niv -- Information-driven, ensemble flexible peptide docking using HADDOCK / Cunliang Geng, Siddarth Narasimhan, João P.G.L.M. Rodrigues, and Alexandre M.J.J. Bonvin -- Modeling peptide-protein structure and binding using Monte Carlo sampling approaches : rosetta FlexPepDock and FlexPepBind / Nawsad Alam and Ora Schueler-Furman -- Flexible backbone methods for predicting and designing peptide specificity / Noah Ollikainen -- Simplifying the design of protein-peptide Interaction specificity with sequence-based representations of atomistic models / Fan Zheng and Gevorg Grigoryan -- Binding specificity profiles from computational peptide screening / Stefan Wallin -- Enriching peptide libraries for binding affinity and specificity through computationally directed library design / Glenna Wink Foight, T. Scott Chen, Daniel Richman, and Amy E. Keating -- Investigating protein-peptide interactions using the Schrödinger computational suite / Jas Bhachoo and Thijs Beuming -- Identifying loop-mediated protein-protein interactions using LoopFinder / Timothy R. Siegert, Michael Bird, and Joshua A. Kritzer -- Protein-peptide interaction design : PepCrawler and PinaColada / Daniel Zaidman and Haim J. Wolfson -- Modeling and design of peptidomimetics to modulate protein-protein interactions / Andrew M. Watkins, Richard Bonneau, and Paramjit S. Arora.
Summary:
This volume covers an array of techniques available for studying peptide-protein docking and design. The book is divided into four sections: peptide binding site prediction; peptide-protein docking; prediction and design of peptide binding specificity; and the design of inhibitory peptides. The chapters in Modeling Peptide-Protein Interactions: Methods and Protocols cover topics such as the usage of ACCLUSTER and PeptiMap for peptide binding site prediction; AnchorDock and ATTRACT for blind, flexible docking of peptides to proteins; flexible peptide docking using HADDOCK and FlexPepDock; identifying loop-mediated protein-protein interactions using LoopFinder; and protein-peptide interaction design using PinaColada. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary details for successful application of the different approaches and step-by-step, readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Modeling Peptide-Protein Interactions: Methods and Protocols provides a diverse and unified overview of this rapidly advancing field of major interest and applicability.
Series:
Methods in molecular biology, 1064-3745 ; 1561 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.