Modeling Protein Interactions with Designed Peptides
Author | : Lisa Ann Eidenschink |
Publisher | : |
Total Pages | : 180 |
Release | : 2009 |
Genre | : Peptides |
ISBN | : |
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Author | : Lisa Ann Eidenschink |
Publisher | : |
Total Pages | : 180 |
Release | : 2009 |
Genre | : Peptides |
ISBN | : |
Author | : Ora Schueler-Furman |
Publisher | : Methods in Molecular Biology |
Total Pages | : 324 |
Release | : 2019-03-13 |
Genre | : Science |
ISBN | : 9781493983025 |
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.
Author | : Martin Zacharias |
Publisher | : World Scientific |
Total Pages | : 401 |
Release | : 2010 |
Genre | : Science |
ISBN | : 184816338X |
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.
Author | : Chao Yu |
Publisher | : |
Total Pages | : 234 |
Release | : 2003 |
Genre | : |
ISBN | : |
Author | : Luca Domenico D’Andrea |
Publisher | : Frontiers Media SA |
Total Pages | : 135 |
Release | : 2021-12-06 |
Genre | : Science |
ISBN | : 2889718204 |
Author | : Knud Jensen |
Publisher | : John Wiley & Sons |
Total Pages | : 306 |
Release | : 2009-09-01 |
Genre | : Science |
ISBN | : 9780470749715 |
Peptides serve as effective drugs in the clinic today. However the inherent drawbacks of peptide structures can limit their efficacy as drugs. To overcome this researchers are developing new methods to create ‘tailor-made’ peptides and proteins with improved pharmacological properties. Design of Peptides and Proteins provides an overview of the experimental and computational methods for peptide and protein design, with an emphasis on specific applications for therapeutics and biomedical research. Topics covered include: Computer modeling of peptides and proteins Peptidomimetics Design and synthesis of cyclic peptides Carbohydrates in peptide and protein design De novo design of peptides and proteins Medical development applications An extended case study – the design of insulin variants Design of Peptides and Proteins presents the state-of-the-art of this exciting approach for therapeutics, with contributions from international experts. It is an essential resource for academic and industrial scientists in the fields of peptide and protein drug design, biomedicine, biochemistry, biophysics, molecular modelling, synthetic organic chemistry and medicinal/pharmaceutical chemistry.
Author | : Vincent Xue |
Publisher | : |
Total Pages | : 164 |
Release | : 2018 |
Genre | : |
ISBN | : |
Protein-protein interactions (PPIs) play a major role in cellular function, mediating signal processing and regulating enzymatic activity. Understanding how proteins interact is essential for predicting new binding partners and engineering new functions. Mutational analysis is one way to study the determinants of protein interaction. Traditionally, the biophysical study of protein interactions has been limited by the number of mutants that could be made and analyzed, but advances in high-throughput sequencing have enabled rapid assessment of thousands of variants. The Keating lab has developed an experimental protocol that can rank peptides based on their binding affinity for a designated receptor. This technique, called SORTCERY, takes advantage of cell sorting and deep-sequencing technologies to provide more binding data at a higher resolution than has previously been achievable. New computational methods are needed to process and analyze the high-throughput datasets. In this thesis, I show how experimental data from SORTCERY experiments can be processed, modeled, and used to design novel peptides with select specificity characteristics. I describe the computational pipeline that I developed to curate the data and regression models that I constructed from the data to relate protein sequence to binding. I applied models trained on experimental data sets to study the peptide-binding specificity landscape of the Bc1-xL, Mc1-1, and Bf1-1 anti-apoptotic proteins, and I designed novel peptides that selectively bind tightly to only one of these receptors, or to a pre-specified combination of receptors. My thesis illustrates how data-driven models combined with high-throughput binding assays provide new opportunities for rational design.
Author | : John Joseph Langone |
Publisher | : Gulf Professional Publishing |
Total Pages | : 864 |
Release | : 1991 |
Genre | : Antigen-antibody reactions |
ISBN | : 9780121821036 |
Computer-based design and modeling, computational approaches, and instrumental methods for elucidating molecular mechanisms of protein folding and ligand-acceptor interactions are included in Volumes 202 and 203, as are genetic and chemical methods for the production of functional molecules including antibodies and antigens, enzymes, receptors, nucleic acids and polysaccharides, and drugs.
Author | : Rossen Donev |
Publisher | : Academic Press |
Total Pages | : 316 |
Release | : 2020-05-01 |
Genre | : Science |
ISBN | : 0128168463 |
Protein Interactions as Targets in Drug Discovery, Volume 121, is dedicated to the design of therapeutics, both experimental and computational, that target protein interactions. Chapters in this new release include Trends in structure based drug design with protein targets, From fragment- to peptide-protein interaction: addressing the structural basis of binding using Supervised Molecular Dynamics (SuMD), Protein-protein and protein-ligand interactions: identification of potential inhibitors through computational analysis, Aromatic-aromatic interactions in protein-drug and protein-protein interactions, Role of protein-protein interaction in allosteric drug design within the human methyltransferome, and much more. Integrates experimental and computational methods for studying protein interactions and their modulation by potential therapeutics Contains timely chapters written by well-renown authorities in their field Covers information that is well supported by a number of high quality illustrations, figures and tables Targets a very wide audience of specialists, researchers and students
Author | : Nir London |
Publisher | : |
Total Pages | : |
Release | : 2011 |
Genre | : Peptide drugs |
ISBN | : |