Protein-Protein and Domain-Domain Interactions

Protein-Protein and Domain-Domain Interactions
Author: Pandjassarame Kangueane
Publisher: Springer
Total Pages: 216
Release: 2018-02-16
Genre: Medical
ISBN: 9811073473
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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.

Protein-protein Complexes

Protein-protein Complexes
Author: Martin Zacharias
Publisher: World Scientific
Total Pages: 401
Release: 2010
Genre: Science
ISBN: 1848163398
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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.

Proteomics and Protein-Protein Interactions

Proteomics and Protein-Protein Interactions
Author: Gabriel Waksman
Publisher: Springer Science & Business Media
Total Pages: 325
Release: 2006-12-22
Genre: Medical
ISBN: 0387245324
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Gabriel Waksman Institute of Structural Molecular Biology, Birkbeck and University College London, Malet Street, London WC1E 7HX, United Kingdom Address for correspondence: Professor Gabriel Waksman Institute of Structural Molecular Biology Birkbeck and University College London Malet Street London WC1E 7H United Kingdom Email: g. waksman@bbk. ac. uk and g. waksman@ucl. ac. uk Phone: (+44) (0) 207 631 6833 Fax: (+44) (0) 207 631 6833 URL: http://people. cryst. bbk. ac. uk/?ubcg54a Gabriel Waksman is Professor of Structural Molecular Biology at the Institute of Structural Molecular Biology at UCL/Birkbeck, of which he is also the director. Before joining the faculty of UCL and Birkbeck, he was the Roy and Diana Vagelos Professor of Biochemistry and Molecular Biophysics at the Washington University School of Medicine in St Louis (USA). The rapidly evolving ?eld of protein science has now come to realize the ubiquity and importance of protein–protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of hi- throughput proteomics to monitor protein–protein interactions at an organism level, we can now safely state that protein–protein interactions are the norm and not the exception.

Protein-Protein Docking

Protein-Protein Docking
Author: Agnieszka A. Kaczor
Publisher: Springer Nature
Total Pages: 360
Release:
Genre:
ISBN: 1071639854
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Protein Interactions: Computational Methods, Analysis And Applications

Protein Interactions: Computational Methods, Analysis And Applications
Author: M Michael Gromiha
Publisher: World Scientific
Total Pages: 424
Release: 2020-03-05
Genre: Science
ISBN: 9811211884
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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.

Glowworm Swarm Optimization

Glowworm Swarm Optimization
Author: Krishnanand N. Kaipa
Publisher: Springer
Total Pages: 265
Release: 2017-01-10
Genre: Technology & Engineering
ISBN: 3319515950
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This book provides a comprehensive account of the glowworm swarm optimization (GSO) algorithm, including details of the underlying ideas, theoretical foundations, algorithm development, various applications, and MATLAB programs for the basic GSO algorithm. It also discusses several research problems at different levels of sophistication that can be attempted by interested researchers. The generality of the GSO algorithm is evident in its application to diverse problems ranging from optimization to robotics. Examples include computation of multiple optima, annual crop planning, cooperative exploration, distributed search, multiple source localization, contaminant boundary mapping, wireless sensor networks, clustering, knapsack, numerical integration, solving fixed point equations, solving systems of nonlinear equations, and engineering design optimization. The book is a valuable resource for researchers as well as graduate and undergraduate students in the area of swarm intelligence and computational intelligence and working on these topics.

Modeling Peptide-Protein Interactions

Modeling Peptide-Protein Interactions
Author: Ora Schueler-Furman
Publisher: Humana
Total Pages: 0
Release: 2017-02-27
Genre: Science
ISBN: 9781493967964
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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.

Intelligent Computing Theories and Application

Intelligent Computing Theories and Application
Author: De-Shuang Huang
Publisher: Springer
Total Pages: 932
Release: 2018-08-08
Genre: Computers
ISBN: 3319959301
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This two-volume set LNCS 10954 and LNCS 10955 constitutes - in conjunction with the volume LNAI 10956 - the refereed proceedings of the 14th International Conference on Intelligent Computing, ICIC 2018, held in Wuhan, China, in August 2018. The 275 full papers and 72 short papers of the three proceedings volumes were carefully reviewed and selected from 632 submissions. The papers are organized in topical sections such as Neural Networks.- Pattern Recognition.- Image Processing.- Intelligent Computing in Robotics.- Intelligent Control and Automation.- Intelligent Data Analysis and Prediction.- Fuzzy Theory and Algorithms.- Supervised Learning.- Unsupervised Learning.- Kernel Methods and Supporting Vector Machines.- Knowledge Discovery and Data Mining.- Natural Language Processing and Computational Linguistics.- Gene Expression Array Analysis.- Systems Biology.- Computational Genomics.- Computational Proteomics.- Gene Regulation Modeling and Analysis.- Protein-Protein Interaction Prediction.- Next-Gen Sequencing and Metagenomics.- Structure Prediction and Folding.- Evolutionary Optimization for Scheduling.- High-Throughput Biomedical Data Integration and Mining.- Machine Learning Algorithms and Applications.- Heuristic Optimization Algorithms for Real-World Applications.- Evolutionary Multi-Objective Optimization and Its Applications.- Swarm Evolutionary Algorithms for Scheduling and Combinatorial.- Optimization.- Swarm Intelligence and Applications in Combinatorial Optimization.- Advances in Metaheuristic Optimization Algorithm.- Advances in Image Processing and Pattern Recognition Techniques.- AI in Biomedicine.- Bioinformatics.- Biometrics Recognition.- Information Security.- Virtual Reality and Human-Computer Interaction.- Healthcare Informatics Theory and Methods.- Intelligent Computing in Computer Vision.- Intelligent Agent and Web Applications.- Reinforcement Learning.- Machine Learning.- Modeling, Simulation, and Optimization of Biological Systems.- Biomedical Data Modeling and Mining.- Cheminformatics.- Intelligent Computing in Computational Biology.- Protein Structure and Function Prediction.- Biomarker Discovery.- Hybrid Computational Intelligence: Theory and Application in Bioinformatics, Computational Biology and Systems Biology.- IoT and Smart Data.- Intelligent Systems and Applications for Bioengineering.- Evolutionary Optimization: Foundations and Its Applications to Intelligent Data Analytics.- Protein and Gene Bioinformatics: Analysis, Algorithms and Applications.

Protein-Ligand Interactions

Protein-Ligand Interactions
Author: Holger Gohlke
Publisher: John Wiley & Sons
Total Pages: 361
Release: 2012-05-21
Genre: Medical
ISBN: 3527329668
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Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.

Protein-protein Recognition

Protein-protein Recognition
Author: Colin Kleanthous
Publisher: Frontiers in Molecular Biology
Total Pages: 370
Release: 2000
Genre: Carrier proteins
ISBN: 9780199637607
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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.