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Protein Interactions: Computational Methods, Analysis And Applications

Author : M Michael Gromiha

Publisher : World Scientific

Page : 424 pages

File Size : 16,87 MB

Release : 2020-03-05

Category : Science

ISBN : 9811211884

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Book Description

This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.



Protein-Protein Interactions

Author : Weibo Cai

Publisher : BoD – Books on Demand

Page : 488 pages

File Size : 42,60 MB

Release : 2012-03-30

Category : Science

ISBN : 9535103970

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Book Description

Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.



Protein Interaction Networks

Author : Aidong Zhang

Publisher : Cambridge University Press

Page : 283 pages

File Size : 18,19 MB

Release : 2009-04-06

Category : Computers

ISBN : 1139479032

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Book Description

The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.



Computational Methods in Protein Evolution

Author : Tobias Sikosek

Publisher : Humana

Page : 0 pages

File Size : 12,87 MB

Release : 2018-10-09

Category : Science

ISBN : 9781493987351

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Book Description

This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.



Protein'Ligand Interactions

Author : G. Ulrich Nienhaus

Publisher : Humana Press

Page : 568 pages

File Size : 30,39 MB

Release : 2005-03-21

Category : Science

ISBN : 9781588293725

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Book Description

A readily reproducible collection of established and emerging techniques for studying the interaction between proteins and ligands, including biochemical/bulk techniques, structure analysis, spectroscopy, single-molecule studies, and theoretical/computational tools. Among the highlights are surface plasmon resonance (SPR) and reflectometric biosensor approaches, high-throughput screening with confocal optics microscopy, single molecule fluorescence and fluorescence correlation spectroscopy (FCS), atomic force microscopy (AFM), crystallography of reaction intermediates, and time-resolved x-ray crystallography. The protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.



Protein-protein Complexes

Author : Martin Zacharias

Publisher : World Scientific

Page : 401 pages

File Size : 11,63 MB

Release : 2010

Category : Science

ISBN : 1848163398

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Book Description

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.



Computational Methods With Applications In Bioinformatics Analysis

Author : Jeffrey J P Tsai

Publisher : World Scientific

Page : 233 pages

File Size : 49,43 MB

Release : 2017-06-09

Category : Science

ISBN : 981320799X

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Book Description

This compendium contains 10 chapters written by world renowned researchers with expertise in semantic computing, genome sequence analysis, biomolecular interaction, time-series microarray analysis, and machine learning algorithms.The salient feature of this book is that it highlights eight types of computational techniques to tackle different biomedical applications. These techniques include unsupervised learning algorithms, principal component analysis, fuzzy integral, graph-based ensemble clustering method, semantic analysis, interolog approach, molecular simulations and enzyme kinetics.The unique volume will be a useful reference material and an inspirational read for advanced undergraduate and graduate students, computer scientists, computational biologists, bioinformatics and biomedical professionals.



Issues in Proteins and Peptides Research and Application: 2011 Edition

Author :

Publisher : ScholarlyEditions

Page : 1761 pages

File Size : 28,25 MB

Release : 2012-01-09

Category : Science

ISBN : 1464964963

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Book Description

Issues in Proteins and Peptides Research and Application: 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Proteins and Peptides Research and Application. The editors have built Issues in Proteins and Peptides Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Proteins and Peptides Research and Application in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Issues in Proteins and Peptides Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.



Protein Interactions as Targets in Drug Discovery

Author : Rossen Donev

Publisher : Academic Press

Page : 318 pages

File Size : 46,33 MB

Release : 2020-04-18

Category : Science

ISBN : 0128168471

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Book Description

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



Explainable AI: Interpreting, Explaining and Visualizing Deep Learning

Author : Wojciech Samek

Publisher : Springer Nature

Page : 435 pages

File Size : 45,8 MB

Release : 2019-09-10

Category : Computers

ISBN : 3030289540

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Book Description

The development of “intelligent” systems that can take decisions and perform autonomously might lead to faster and more consistent decisions. A limiting factor for a broader adoption of AI technology is the inherent risks that come with giving up human control and oversight to “intelligent” machines. For sensitive tasks involving critical infrastructures and affecting human well-being or health, it is crucial to limit the possibility of improper, non-robust and unsafe decisions and actions. Before deploying an AI system, we see a strong need to validate its behavior, and thus establish guarantees that it will continue to perform as expected when deployed in a real-world environment. In pursuit of that objective, ways for humans to verify the agreement between the AI decision structure and their own ground-truth knowledge have been explored. Explainable AI (XAI) has developed as a subfield of AI, focused on exposing complex AI models to humans in a systematic and interpretable manner. The 22 chapters included in this book provide a timely snapshot of algorithms, theory, and applications of interpretable and explainable AI and AI techniques that have been proposed recently reflecting the current discourse in this field and providing directions of future development. The book is organized in six parts: towards AI transparency; methods for interpreting AI systems; explaining the decisions of AI systems; evaluating interpretability and explanations; applications of explainable AI; and software for explainable AI.