Protein Interactions: Computational Methods, Analysis And Applications
Protein Interactions: Computational Methods, Analysis And Applications

Author: M Michael Gromiha

Publisher: World Scientific

Published: 2020-03-05

Total Pages: 424

ISBN-13: 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.

Protein-Protein Interactions
Protein-Protein Interactions

Author: Weibo Cai

Publisher: BoD – Books on Demand

Published: 2012-03-30

Total Pages: 488

ISBN-13: 9535103970

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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
Protein Interaction Networks

Author: Aidong Zhang

Publisher: Cambridge University Press

Published: 2009-04-06

Total Pages: 283

ISBN-13: 1139479032

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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.

Biological Data Mining in Protein Interaction Networks
Biological Data Mining in Protein Interaction Networks

Author: Li, Xiao-Li

Publisher: IGI Global

Published: 2009-05-31

Total Pages: 448

ISBN-13: 1605663999

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"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.

Protein'Ligand Interactions
Protein'Ligand Interactions

Author: G. Ulrich Nienhaus

Publisher: Humana Press

Published: 2005-03-21

Total Pages: 568

ISBN-13: 9781588293725

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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
Protein-protein Complexes

Author: Martin Zacharias

Publisher: World Scientific

Published: 2010

Total Pages: 401

ISBN-13: 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.

Computational Methods in Protein Evolution
Computational Methods in Protein Evolution

Author: Tobias Sikosek

Publisher: Humana

Published: 2018-10-09

Total Pages: 0

ISBN-13: 9781493987351

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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.

Computational Structural Biology
Computational Structural Biology

Author: Torsten Schwede

Publisher: World Scientific

Published: 2008

Total Pages: 790

ISBN-13: 9812778780

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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.

Protein-protein Interactions
Protein-protein Interactions

Author: Erica A. Golemis

Publisher: CSHL Press

Published: 2005

Total Pages: 954

ISBN-13: 0879697237

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Reflecting the various advances in the field, this book provides comprehensive coverage of protein-protein interactions. It presents a collection of the technical and theoretical issues involved in the study of protein associations, including biophysical approaches. It also offers a collection of computational methods for analyzing interactions.

Computational and Structural Approaches to Drug Discovery
Computational and Structural Approaches to Drug Discovery

Author: Robert M. Stroud

Publisher: Royal Society of Chemistry

Published: 2008

Total Pages: 171

ISBN-13: 0854043659

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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.