Download or read book Structural Bioinformatics written by Jenny Gu and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 1105 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Advance in Structural Bioinformatics written by Dongqing Wei and published by Springer. This book was released on 2014-11-11 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Download or read book Structural Bioinformatics Applications in Preclinical Drug Discovery Process written by C. Gopi Mohan and published by Springer. This book was released on 2019-01-10 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

Download or read book Structural Bioinformatics written by Forbes J. Burkowski and published by CRC Press. This book was released on 2008-10-30 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Beauty of Protein Structures and the Mathematics behind Structural BioinformaticsProviding the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure.Helps Students Go Further in Their Study of Structural Biolog

Download or read book Bayesian Methods in Structural Bioinformatics written by Thomas Hamelryck and published by Springer. This book was released on 2012-03-23 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an edited volume, the goal of which is to provide an overview of the current state-of-the-art in statistical methods applied to problems in structural bioinformatics (and in particular protein structure prediction, simulation, experimental structure determination and analysis). It focuses on statistical methods that have a clear interpretation in the framework of statistical physics, rather than ad hoc, black box methods based on neural networks or support vector machines. In addition, the emphasis is on methods that deal with biomolecular structure in atomic detail. The book is highly accessible, and only assumes background knowledge on protein structure, with a minimum of mathematical knowledge. Therefore, the book includes introductory chapters that contain a solid introduction to key topics such as Bayesian statistics and concepts in machine learning and statistical physics.

Download or read book Bioinformatics Sequences Structures Phylogeny written by Asheesh Shanker and published by Springer. This book was released on 2018-10-13 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Recent Advances in Structural Bioinformatics 2007 written by Alexandre G. de Brevern and published by . This book was released on 2007-01-01 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first mention of the word protein was from a letter sent by Jöns Jakob Berzelius to Gerhardus Johannes Mulder on 10. July 1838, where he wrote: The name protein that I propose for the organic oxide of fibrin and albumin, I wanted to derive from p??te???, [protas meaning of primary importance ] because it appears to be the primitive or principal substance of animal nutrition. A protein is a complex, high-molecular-mass, organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Different proteins perform a wide variety of biological functions. Some proteins are enzymes, which catalyze chemical reactions. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton, which is like a system of scaffolding within a cell. Still more functions filled by proteins include immune response and the storage and transport of various ligands. Proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Thus, proteins are their own polymers, with amino acids being the monomers. We can refer to four distinct aspects of a protein's structure: (i) Primary structure: the amino acid sequence, (ii) Secondary structure: highly patterned sub-structures, (iii) Tertiary structure: the overall shape of a single protein molecule, (iv) Quaternary structure: the shape or structure that results from the interaction of more than one protein molecule, usually called protein subunits in this context, which function as part of the larger assembly or protein complex. The knowledge of protein structures can help in numerous cases, e.g. to annotate unknown function, to understand the function mechanism and so their dysfunctions, to design drugs, to propose new evolutionary prospects... In 1951, Pauling and Corey performed seven studies published back-to-back, all on the subject of protein structure, presenting the alpha-helix and the beta-sheet described the polypeptide backbone folding stabilized by hydrogen bonds [1, 2]. In 1958, myoglobin was the first protein structure solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew. This work was acknowledged by a Nobel Prize in Chemistry [3, 4]. Since, the number of available protein structures has grown slowly, and increase greatly this last decade. Despite this progress, the gap between the number of sequences and structures known at the atomic scale is still considerable (3,170,612 protein sequences in UniProt database vs. 39,678 structures in Protein DataBank in August 2006). NMR or X-ray experiments even if being the most appropriate methods to gain such information are in fact strongly limited because of the different unavoidable steps, to be performed initially. Indeed before putting the sample in the experimental devices, one needs to express to extract, and to purify the protein while maintaining its functional properties. This last point is of course the most important one. Such necessity is as much difficult to obey for membrane proteins that frequently denature when extract from their material environment. Not denature approaches are required that could provide details of protein structures. Structural bioinformatics approaches belong to this field. In this book, many researchers present their work on structural bioinformatics and / or structural genomics. The first parts of the book focus on the analysis and prediction of protein structures with classical and innovative approaches (Chapters 1 to 6). The second part of this book focus on new approaches to analyze protein functions using protein structures (Chapters 7 to 11), while last part describe some pertinent examples of globular and transmembrane proteins (Chapters 12 to 16). Benros, Martin et al. present the different aspects of secondary structure assignment and describe the resulting problems (Chapter 1). The following chapter by Tyagi et al. extends this reviewing to novel other approaches, named the structural alphabets, composed of sets or libraries of local structure proteins (Chapter 2). Fuchs et al. present an up-to-date review about the assignment, analysis and prediction of well-characterized local protein structure, the b-turns (Chapter 3). Kondratova and Efimov present the effect of structural context on specificity of polar interactions in proteins, highlighting that differently packed a-helices had distinct interhelical networks of hydrogen and salt bonds (Chapter 4). Roterman et al. present a review about their innovative recent researches on early-stage protein folding using an ellipsoid model (Chapter 5). Carpentier et al. present a review the structural similarity detection and especially at a large scale within a database (Chapter 6). Reuter reviews the different know approaches dedicated to Normal Mode Analyses and the corresponding existing databases and web services (Chapter 7). Baaden and Lavery in their review highlight the constraints imposed by the size, time and energy scales of biomolecules depending on the range and details of the performed simulations (Chapter 8). Autin, Montes et al. reviews an impressive number of docking tools dedicated to protein-protein docking and virtual ligand screening methods highlighting the problem and challenges of this research area (Chapter 9). Bastard and Prévost focus their review on the difficult case of flexible macromolecular docking (Chapter 10). Loch reviews structure-based virtual screening process detailing the various in silico methods used (Chapter 11). Gowri et al. present the application and challenges of comparative modeling applied at the genomic scale (Chapter 12). Krupa and Srinivasan develop an analysis about the evolution of FAD synthetases and associated functional domains (Chapter 13), while Bhaduri and John focus on the particular case of the Protein O-Phosphatase families (Chapter 14). Transmembrane structures are available in very few numbers, thus Simoes et al. show the different aspect of homology modeling in the case of Kca3.1 calcium activated K+ channel and of Ca2+ selective voltage insensitive TRPV5 channel (Chapter 15). Debret and Etchebest review the evolution of the researches and views of a particular mecanosensitive transmembrane protein, the MscL (Chapter 16). This book is dedicated to the memory of Pr. Serge Hazout. He was an excellent scientist who had worked on numerous subjects such as human genetics [5], image pattern [6], sequence alignments [7], protein docking [8], protein side chain prediction [9], and recently developed numerous new approaches dedicated to structural alphabets [10-13] and microarray data analysis [14], but more important, he was greatly human. Chapter 17 present so a review and new developments on a difficult problem: How compare the predictions of more than 2 states? Pr. Serge Hazout presents different known and new statistical criteria to assess the performance of prediction approaches.

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.

Download or read book Structural Bioinformatics 2nd Edition written by Jenny Gu and published by . This book was released on 2009 with total page 1067 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Structural Bioinformatics Tools for Drug Design written by Jaroslav Koča and published by Springer. This book was released on 2017-01-24 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Advances in Bioinformatics written by Vijai Singh and published by Springer Nature. This book was released on 2021-07-31 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the latest developments in bioinformatics, highlighting the importance of bioinformatics in genomics, transcriptomics, metabolism and cheminformatics analysis, as well as in drug discovery and development. It covers tools, data mining and analysis, protein analysis, computational vaccine, and drug design. Covering cheminformatics, computational evolutionary biology and the role of next-generation sequencing and neural network analysis, it also discusses the use of bioinformatics tools in the development of precision medicine. This book offers a valuable source of information for not only beginners in bioinformatics, but also for students, researchers, scientists, clinicians, practitioners, policymakers, and stakeholders who are interested in harnessing the potential of bioinformatics in many areas.

Download or read book Algorithms and Methods in Structural Bioinformatics written by Nurit Haspel and published by Springer Nature. This book was released on 2022-09-01 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Advances in Structural Biology written by S.K. Malhotra and published by Elsevier. This book was released on 2000-03-07 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: In keeping with the broad objectives set for the serial publication of Advances in Structural Biology, Volume 6 contains exhaustive articles from experts in diverse areas of biomedical research. The common thread among the various articles is their relevance to the applications of cell biology to human health.

Download or read book Bioinformatics written by Andreas D. Baxevanis and published by John Wiley & Sons. This book was released on 2004-03-24 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: "In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.

Download or read book Essential Bioinformatics written by Jin Xiong and published by Cambridge University Press. This book was released on 2006-03-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.