Author: Kelly Marie Thayer
Publisher:
ISBN:
Category : Binding sites (Biochemistry)
Languages : en
Pages : 758

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Author: Jenny Gu
Publisher: John Wiley & Sons
ISBN: 1118210565
Category : Science
Languages : en
Pages : 1105

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Book Description
Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics

Author: Jaroslav Koča
Publisher: Springer
ISBN: 3319473883
Category : Medical
Languages : en
Pages : 146

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Book Description
The book describes the individual steps necessary for biomacromolecular fragments analysis, as well as a list of essential software tools. For each step, it also shows corresponding web-based tools in detail and provides practical examples of their use. All tools and databases mentioned in the examples are available free of charge, platform-independent, web-based, user-friendly and do not require a prior IT background to be fully used.

Author: Nurit Haspel
Publisher: Springer Nature
ISBN: 303105914X
Category : Science
Languages : en
Pages : 120

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Book Description
The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved. In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.

Author: Torsten Schwede
Publisher: World Scientific
ISBN: 9814472417
Category : Science
Languages : en
Pages : 790

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Book Description
Computational structural biology has made tremendous progress over the last two decades, and this book provides a recent and broad overview of such computational methods in structural biology. It covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology. In addition to reviewing the current state of computational structural biology, each chapter ends with a brief, visionary discussion on the future outlook, whereby the main challenges for the coming years are elucidated. Written by an international panel of expert contributors, this book can serve as a reference manual for students and practitioners alike.

Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 754

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Author: Daniel John Rigden
Publisher: Springer Science & Business Media
ISBN: 1402090587
Category : Science
Languages : en
Pages : 330

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Book Description
Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Author: Dongqing Wei
Publisher: Springer
ISBN: 9401792453
Category : Science
Languages : en
Pages : 380

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Book Description
This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.

Author: Nancy C. Stellwagen
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 284

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Book Description
Curvature and Deformation of Nucleic Acids: Recent Advances, New Paradigms presents an up-to-date review on the curvature and deformation of nucleic acids. Chapter 1 sets the various chapters in context, as well as describing several controversial topics. Chapter 2 gives a comprehensive review of the literature on DNA bending and describes the current status of molecular dynamics simulations of DNA and protein-DNA complexes. Chapter 3 describes the structural basis for A-tract DNA helix bending, based on recent NMR structures and other biophysical measurements. Chapter 4 describes the localization of Mg++ ions in the crystal structure of a B-form DNA dodecamer and discusses the relevance of these bound ions to sequence-dependent bending. Chapter 5 discusses the electrostatic energy penalties that result from phosphate crowding in curved DNA oligomers. Chapter 6 presents a quantitative model that predicts the magnitude of the bend caused by asymmetric charge neutralization of DNA phosphate residues. Chapter 7 reviews the structural and dynamic properties of four-way DNA junctions in the presence of metal ions, and it describes the exchange between alternative stacking conformers in solution. Chapter 8 documents the fact that a conserved pseudouridine residue in an RNA duplex containing a precursor messenger branch site makes an important contribution to the structure of the molecule. Chapter 9 describes structural perturbations that are observed in disease-related mutants of human mitochondrial transfer RNAs. Chapter 10 reviews the thermodynamics of the folding and unfolding of DNA oligomers distorted by the binding of small ligands. Chapter 11 describes a method of constructing DNA fragments for cyclization studies that uses single strand gaps as flexible hinges that allow the correct torsional orientation of the helix ends. Chapter 12 reviews a statistical mechanical model that predicts the stability of reconstituted nucleosomes based on sequence-dependent DNA curvature and flexibility.

Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1872

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Book Description