Modeling Peptide-Protein Interactions

Methods and Protocols

Häftad, Engelska, 2018

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This volume covers an array of techniques available for studying peptide-protein docking and design.

The Usage of ACCLUSTER for Peptide Binding Site Prediction.- Detection of Peptide-Binding Sites on Protein Surfaces using the Peptimap Server.- Peptide Sub-Optimal Conformation Sampling for the Prediction of Protein-Peptide Interactions.- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock.- Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Protein-Peptide Interactions.- Highly Flexible Protein-Peptide Docking Using CABS-Dock.- AnchorDock for Blind Flexible Docking of Peptides to Proteins.- Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.- Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock & FlexPepBind.- Flexible Backbone Methods for Predicting and Designing Peptide Specificity.- SImplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models.- Binding Specificity Profiles from Computational Peptide Screening.- Enriching Peptide Libraries for Binding Affinity and Specificity through Computationally Directed Library Design.- Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite.- Identifying Loop-Mediated Protein-Protein Interactions using LoopFinder.- Protein-Peptide Interaction Design: PepCrawler and PinaColada.- Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions.