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Computational Approaches For Prediction Of Protein Protein Interaction
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Book Synopsis New Approaches of Protein Function Prediction from Protein Interaction Networks by : Jingyu Hou
Download or read book New Approaches of Protein Function Prediction from Protein Interaction Networks written by Jingyu Hou and published by Academic Press. This book was released on 2017-01-13 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks. Functional annotation of proteins is vital to biological and clinical research and other applications due to the important roles proteins play in various biological processes. Although the functions of some proteins have been annotated via biological experiments, there are still many proteins whose functions are yet to be annotated due to the limitations of existing methods and the high cost of experiments. To overcome experimental limitations, this book helps users understand the computational approaches that have been rapidly developed for protein function prediction. - Provides innovative approaches and new developments targeting key issues in protein function prediction - Presents heuristic ideas for further research in this challenging area
Book Synopsis Protein Interactions: Computational Methods, Analysis And Applications by : M Michael Gromiha
Download or read book Protein Interactions: Computational Methods, Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein Interaction Networks by : Aidong Zhang
Download or read book Protein Interaction Networks written by Aidong Zhang and published by Cambridge University Press. This book was released on 2009-04-06 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein-Protein Interactions by : Weibo Cai
Download or read book Protein-Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Biological Data Mining in Protein Interaction Networks by : Li, Xiao-Li
Download or read book Biological Data Mining in Protein Interaction Networks written by Li, Xiao-Li and published by IGI Global. This book was released on 2009-05-31 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The goal of this book is to disseminate research results and best practices from cross-disciplinary researchers and practitioners interested in, and working on bioinformatics, data mining, and proteomics"--Provided by publisher.
Book Synopsis Explainable AI: Interpreting, Explaining and Visualizing Deep Learning by : Wojciech Samek
Download or read book Explainable AI: Interpreting, Explaining and Visualizing Deep Learning written by Wojciech Samek and published by Springer Nature. This book was released on 2019-09-10 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein-protein Interactions and Networks by : Anna Panchenko
Download or read book Protein-protein Interactions and Networks written by Anna Panchenko and published by Springer Science & Business Media. This book was released on 2010-04-06 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.
Book Synopsis Protein-protein Complexes by : Martin Zacharias
Download or read book Protein-protein Complexes written by Martin Zacharias and published by World Scientific. This book was released on 2010 with total page 401 pages. 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.
Book Synopsis Computational Methods in Protein Evolution by : Tobias Sikosek
Download or read book Computational Methods in Protein Evolution written by Tobias Sikosek and published by Humana. This book was released on 2018-10-09 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Structural Biology by : Torsten Schwede
Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.
Book Synopsis Computational and Structural Approaches to Drug Discovery by : Robert M. Stroud
Download or read book Computational and Structural Approaches to Drug Discovery written by Robert M. Stroud and published by Royal Society of Chemistry. This book was released on 2008 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the physiological factors of pharmacology, a key area, is explored.
Book Synopsis Inhibitors of Protein–Protein Interactions by : Ali Tavassoli
Download or read book Inhibitors of Protein–Protein Interactions written by Ali Tavassoli and published by Royal Society of Chemistry. This book was released on 2020-12-07 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein-protein interactions (PPI) are at the heart of the majority of cellular processes, and are frequently dysregulated or usurped in disease. Given this central role, the inhibition of PPIs has been of significant interest as a means of treating a wide variety of diseases. However, there are inherent challenges in developing molecules capable of disrupting the relatively featureless and large interfacial areas involved. Despite this, there have been a number of successes in this field in recent years using both traditional drug discovery approaches and innovative, interdisciplinary strategies using novel chemical scaffolds. This book comprehensively covers the various aspects of PPI inhibition, encompassing small molecules, peptidomimetics, cyclic peptides, stapled peptides and macrocycles. Illustrated throughout with successful case studies, this book provides a holistic, cutting-edge view of the subject area and is ideal for chemical biologists and medicinal chemists interested in developing PPI inhibitors.
Book Synopsis Multiscale Approaches to Protein Modeling by : Andrzej Kolinski
Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.
Book Synopsis Protein-Protein and Domain-Domain Interactions by : Pandjassarame Kangueane
Download or read book Protein-Protein and Domain-Domain Interactions written by Pandjassarame Kangueane and published by Springer. This book was released on 2018-02-16 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.
Book Synopsis Protein-protein Recognition by : Colin Kleanthous
Download or read book Protein-protein Recognition written by Colin Kleanthous and published by Frontiers in Molecular Biology. This book was released on 2000 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of Protein-Protein Recognition is to bring together concepts and systems pertaining to protein-protein interactions in a single unifying volume. In the light of the information from the genome sequencing projects and the increase in structural information it is an opportune time totry to make generalizations about how and why proteins form complexes with each other. The emphasis of the book is on heteromeric complexes (complexes in which each of the components can exist in an unbound state) and will use well-studied model systems to explain the processes of formingcomplexes. After an introductory section on the kinetics, thermodynamics, analysis, and classification of protein-protein interactions, weak, intermediate, and high affinity complexes are dealt with in turn. Weak affinity complexes are represented by electron transfer proteins and integrincomplexes. Anti-lysozyme antibodies, the MHC proteins and their interactions with T-cell receptors, and the protein interactions of eukaryotic signal transduction are the systems used to explain complexes with intermediate affinities. Finally, tight binding complexes are represented by theinteraction of protein inhibitors with serine proteases and by nuclease inhibitor complexes. Throughout the chapters common themes are the technologies which have had the greatest impact, how specificity is determined, how complexes are stabilized, and medical and industrial applications.
Book Synopsis Target Discovery and Validation by : Alleyn T. Plowright
Download or read book Target Discovery and Validation written by Alleyn T. Plowright and published by John Wiley & Sons. This book was released on 2020-02-18 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: The modern drug developers? guide for making informed choices among the diverse target identification methods Target Discovery and Validation: Methods and Strategies for Drug Discovery offers a hands-on review of the modern technologies for drug target identification and validation. With contributions from noted industry and academic experts, the book addresses the most recent chemical, biological, and computational methods. Additionally, the book highlights techologies that are applicable to ?difficult? targets and drugs directed at multiple targets, including chemoproteomics, activity-based protein profiling, pathway mapping, genome-wide association studies, and array-based profiling. Throughout, the authors highlight a range of diverse approaches, and target validation studies reveal how these methods can support academic and drug discovery scientists in their target discovery and validation research. This resource: -Offers a guide to identifying and validating targets, a key enabling technology without which no new drug development is possible -Presents the information needed for choosing the appropriate assay method from the ever-growing range of available options -Provides practical examples from recent drug development projects, e. g. in kinase inhibitor profiling Written for medicinal chemists, pharmaceutical professionals, biochemists, biotechnology professionals, and pharmaceutical chemists, Target Discovery and Validation explores the current methods for the identification and validation of drug targets in one comrpehensive volume. It also includes numerous practical examples.
Book Synopsis Lipid Peroxidation by : Angel Catalá
Download or read book Lipid Peroxidation written by Angel Catalá and published by Nova Science Publishers. This book was released on 2017 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of lipid peroxidation: inhibition, effects and mechanisms. The topics analyzed, cover a broad spectrum of functions played by lipid peroxidation and presents new information in this area of research. The topics analyzed include: progress in the knowledge of lipid peroxidation, from the first evidences issued by Nicolas Theodore de Saussure in Paris 1804; fighting against lipid peroxidation: the unique story of docosahexaenoic acid in the brain; protective effects of melatonin and structurally-related molecules in reducing membrane rigidity due to lipid peroxidation; synergistic effects of antioxidant compositions during inhibited lipid autoxidation; lipid peroxidation and animal longevity; free radicals in health and disease; lipid peroxidation in autoimmune diseases; aldehydes derived from lipid peroxidation in cancer and autoimmunity; the role of reactive oxygen species and lipid peroxidation in the neurodegenerative process after spinal cord injury; kinetics and mechanisms of inhibited lipid autoxidation in presence of 4-substituted-coumarins; hypoxia and oxidative stress: cell signaling mechanisms and protective role of vitamin C and cilnidipine; characterization of oxidative stress and antioxidant potency; paying attention to time and location; lipid peroxidation in aquatic organisms: ontogenetic, phylogenetic and ecological aspects; chemistry of lipid oxidation in edible oils; and menopause progression and oxidative stress: associated mechanisms and the importance of physical exercise.
