Computational Modeling of Peptide-protein Binding - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Computational Modeling of Peptide-protein Binding write by Jack Scott Emery. This book was released on 2010. Computational Modeling of Peptide-protein Binding available in PDF, EPUB and Kindle. 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.
Modeling Peptide-Protein Interactions
Modeling Peptide-Protein Interactions - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Modeling Peptide-Protein Interactions write by Ora Schueler-Furman. This book was released on 2017-02-27. Modeling Peptide-Protein Interactions available in PDF, EPUB and Kindle. 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.
Computational Modeling of Protein-protein Complexes with Therapeutic Binding Proteins
Computational Modeling of Protein-protein Complexes with Therapeutic Binding Proteins - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Computational Modeling of Protein-protein Complexes with Therapeutic Binding Proteins write by Filip Radom. This book was released on 2019. Computational Modeling of Protein-protein Complexes with Therapeutic Binding Proteins available in PDF, EPUB and Kindle.
Computational Design of Ligand Binding Proteins
Computational Design of Ligand Binding Proteins - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Computational Design of Ligand Binding Proteins write by Barry L. Stoddard. This book was released on 2016-04-20. Computational Design of Ligand Binding Proteins available in PDF, EPUB and Kindle. This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Peptides Targeting Protein-Protein Interactions: Methods and Applications
Peptides Targeting Protein-Protein Interactions: Methods and Applications - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Peptides Targeting Protein-Protein Interactions: Methods and Applications write by Luca Domenico D’Andrea. This book was released on 2021-12-06. Peptides Targeting Protein-Protein Interactions: Methods and Applications available in PDF, EPUB and Kindle.
