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Modeling Peptide-Protein Interactions: Methods and Protocols

2019-03-13 Science
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Release : 2019-03-13
Genre : Science
Kind : eBook
Book Rating : 025/5 ( reviews)

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Book Synopsis Modeling Peptide-Protein Interactions: Methods and Protocols by : Ora Schueler-Furman

Download or read book Modeling Peptide-Protein Interactions: Methods and Protocols written by Ora Schueler-Furman. This book was released on 2019-03-13. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein-protein Complexes

2010 Science
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Release : 2010
Genre : Science
Kind : eBook
Book Rating : 38X/5 ( reviews)

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Book Synopsis Protein-protein Complexes by : Martin Zacharias

Download or read book Protein-protein Complexes written by Martin Zacharias. This book was released on 2010. Available in PDF, EPUB and Kindle. Book excerpt: Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Characterization, Modeling and Manipulation of Peptide-protein Interactions

2011 Peptide drugs
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Release : 2011
Genre : Peptide drugs
Kind : eBook
Book Rating : /5 ( reviews)

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Book Synopsis Characterization, Modeling and Manipulation of Peptide-protein Interactions by : Nir London

Download or read book Characterization, Modeling and Manipulation of Peptide-protein Interactions written by Nir London. This book was released on 2011. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Modeling of Peptide-protein Binding

2010 Chemical affinity
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Release : 2010
Genre : Chemical affinity
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Book Synopsis Computational Modeling of Peptide-protein Binding by : Jack Scott Emery

Download or read book Computational Modeling of Peptide-protein Binding written by Jack Scott Emery. This book was released on 2010. Available in PDF, EPUB and Kindle. Book excerpt: Peptides offer great promise as targeted affinity ligands, but the space of possible peptide sequences is vast, making experimental identification of lead candidates expensive, difficult, and uncertain. Computational modeling can narrow the search by estimating the affinity and specificity of a given peptide in relation to a predetermined protein target. The predictive performance of computational models of interactions of intermediate-length peptides with proteins can be improved by taking into account the stochastic nature of the encounter and binding dynamics. A theoretical case is made for the hypothesis that, because of the flexibility of the peptide and the structural complexity of the target protein, interactions are best characterized by an ensemble of possible bound configurations rather than a single & ldquo;lock and key & rdquo; fit. A model incorporating these factors is proposed and evaluated. A comprehensive dataset of 3,924 peptide-protein interface structures was extracted from the Protein Data Bank (PDB) and descriptors were computed characterizing the geometry and energetics of each interface. The characteristics of these interfaces are shown to be generally consistent with the proposed model, and heuristics for design and selection of peptide ligands are derived. The curated and energy-minimized interface structure dataset and a relational database containing the detailed results of analysis and energy modeling are made publicly available via a web repository. A novel analytical technique based on the proposed theoretical model, Virtual Scanning Probe Mapping (VSPM), is implemented in software to analyze the interaction between a target protein of known structure and a peptide of specified sequence, producing a spatial map indicating the most likely peptide binding regions on the protein target. The resulting predictions are shown to be superior to those of two other published methods, and support the validity of the stochastic binding model.

Peptides Targeting Protein-Protein Interactions: Methods and Applications

2021-12-06 Science
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Release : 2021-12-06
Genre : Science
Kind : eBook
Book Rating : 204/5 ( reviews)

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Book Synopsis Peptides Targeting Protein-Protein Interactions: Methods and Applications by : Luca Domenico D’Andrea

Download or read book Peptides Targeting Protein-Protein Interactions: Methods and Applications written by Luca Domenico D’Andrea. This book was released on 2021-12-06. Available in PDF, EPUB and Kindle. Book excerpt:

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