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[转载] Manish Bhojasia推荐的十本 Best Reference Books on[计算结构生物] 书单

已有 2273 次阅读 2022-4-29 19:54 |系统分类:科研笔记|文章来源:转载

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https://www.sanfoundry.com/best-reference-books-structural-biology:

Structural Biology Books

"We have compiled the list of Best Reference Books on Structural Biology subject. These books are used by students of top universities, institutes and colleges. Here is the full list of best books on Structural Biology along with reviews.

Kindly note that we have put a lot of effort into researching the best books on Structural Biology subject and came out with a recommended list of best books. The table below contains the Name of these best books, their authors, publishers and an unbiased review of books on “Structural Biology” as well as links to the Amazon website to directly purchase these books. As an Amazon Associate, we earn from qualifying purchases, but this does not impact our reviews, comparisons, and listing of these top books; the table serves as a ready reckoner list of these best books.

List of Structural Biology Books with author’s names, publishers, and an unbiased review as well as links to the Amazon website to directly purchase these books.

"

  • Structural Biology

  • Computational Structural Biology


1. Structural Biology


1. “Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology” by Bernhard Rupp

“Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology” Book Review: This book describes the fundamentals, practices, and applications of protein crystallography. This book has been illustrated in full-color. The book describes mathematical and physical concepts in accessible and accurate language. It highlights key concepts for understanding the practice and analysis of protein crystal structures. The book contains examples of biologically-relevant molecules, complexes, and drug target structures. This book will be a valuable resource for advanced undergraduate and graduate students and practitioners in structural biology, crystallography, and structural bioinformatics.

2. “Structure And Action Of Molecular Chaperones: Machines That Assist Protein Folding In The Cell: 6 (Series in Structural Biology)” by Lila M Gierasch and Arthur L Horwich

“Structure And Action Of Molecular Chaperones: Machines That Assist Protein Folding In The Cell: 6 (Series in Structural Biology)” Book Review: This book reviews the beautiful architectures and varying mechanical actions of the set of specialized cellular proteins called molecular chaperones. It provides essential kinetic assistance to processes of protein folding and unfolding in the cell. The book illustrates each type of chaperone by X-ray and EM structure determinations at near- atomic level resolution. It is described by a leader in the study of the respective family. This book can be used by students and researchers of structural biology.

3. “Introduction to Protein Architecture: The Structural Biology of Proteins” by Arthur M Lesk

“Introduction to Protein Architecture: The Structural Biology of Proteins” Book Review: This book is written in a clear and engaging style and has several illustrations with computer graphics. The emphasis of this book is on protein architecture, on proteins as three-dimensional patterns. This book introduces the use of the World Wide Web in bioinformatics. This book explains the general characteristics of proteins that underlie the great variety of folding patterns observed in nature. This book is for second and third year undergraduate students and beginning postgraduate students. It will be of interest to all biological and medical scientists whose work touches on proteins.

4. “Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology)” by Gordon S Rule and T Kevin Hitchens

Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology)” Book Review: This book helps study the structure and dynamics of biological macromolecules. This book gives a basic understanding of the phenomenological properties of magnetic resonance. The book also explains the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. The book begins with elementary quantum mechanics where a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multinuclear NMR pulse sequences. The book gives a modular analysis of NMR pulse sequence building blocks which provides a basis for understanding and developing novel pulse programs. It covers topics from chemical shift assignment to protein structure refinement to the analysis of protein dynamics and chemical kinetics. The book also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. There are end of chapter exercises that are included to emphasize important concepts. This book offers students a systematic, in-depth, understanding of modern NMR spectroscopy. The application of this book to biomolecular systems will also be useful for the experienced investigator.

5. “Structural Aspects of Protein Synthesis: (Series in Structural Biology)” by Liljas Anders

“Structural Aspects of Protein Synthesis: (Series in Structural Biology)” Book Review: This book provides a description of the structure and function of the translation system including ribosomes, tRNAs, translation factors, antibiotics and aminoacyl-tRNA synthetases. The structural research by crystallography and cryo-EM forms part of an interactive framework that involves biochemistry and molecular computation. The book provides a detailed overview of translation in light of the structural results. It is a valuable resource for scientists in this and related fields, as well as for students taking courses with a focus on translation.

6. “Molecular Structures and Structural Dynamics of Prion Proteins and Prions (Focus on Structural Biology)” by Jiapu Zhang  - see  Molecular Structures and Structural Dynamics of Prion Proteins and Prions | SpringerLink

“Molecular Structures and Structural Dynamics of Prion Proteins and Prions (Focus on Structural Biology)” Book Review: This is an easy-to-read-and-understand book on prion proteins’ molecular dynamics (MD) simulations and on prions’ molecular modelling (MM) constructions. This book enables researchers to see what is crucial to the conformational change from normal cellular prion protein (PrPC) to diseased infectious prions (PrPSc), using MD and MM techniques. This book’s MD studies on species are helpful to understand the mechanism underlying the resistance to prion diseases. This book also studies the unstructured region through MD and especially MM techniques from the global optimization point of view. This book is ideal for practitioners in computing of biophysics, biochemistry, biomedicine, bioinformatics and cheminformatics. It is also useful for practitioners and students in materials science and engineering, applied mathematics and theoretical physics, information technology, operations research, biostatistics, etc.

      



7. “Structural Genomics (Methods in Molecular Biology)” by Yu Wai Chen

“Structural Genomics (Methods in Molecular Biology)” Book Review: This book emphasizes the benefits of Structural Genomics to the wider structural research community. It also reflects the current trend in tackling the challenges of studying macromolecular machineries and complexes. The topics in this book include the cloning and production of proteins for structural studies, experimental methods, and computational methods and data analysis. The chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. This book is authoritative and easily accessible. This book aims to channel spin-off technologies to the average structural biologist in a small or medium-sized laboratory.

8. “Structural Proteomics (Methods in Molecular Biology)” by Raymond J Owens

“Structural Proteomics (Methods in Molecular Biology)” Book Review: This book shows the current state of the structural protein field with improved and refined protocols that have been applied to particularly challenging proteins. This book explores the resources available for curation, annotation, and structure prediction in silico. This book has methods for sample preparation of both proteins and crystals as well as structural characterization techniques. The chapters in this book include introductions to their respective topics, lists of the necessary materials and reagents. It also has step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. This book will help researchers in expanding knowledge of this vital and expansive area of protein science.

9. “Structural Proteomics: High-Throughput Methods (Methods in Molecular Biology)” Structural Proteomics: High-Throughput Methods (Methods in Molecular Biology)

“Structural Proteomics: High-Throughput Methods (Methods in Molecular Biology)” Book Review: This book provides a current view of all aspects of the ‘pipeline’ that takes protein targets to structures and how these have been optimised. This book includes chapters describing, in-depth, the individual steps in the Structural Genomics pipeline. It also has less detailed overviews of individual Structural Genomics initiatives. This book covers techniques in a new and emerging field. This book will be helpful to researchers and students in this field.

10. “Data Mining in Structural Biology: Signal Transduction and Beyond (Ernst Schering Foundation Symposium Proceedings)” by U Egner and I Schlichting

“Data Mining in Structural Biology: Signal Transduction and Beyond (Ernst Schering Foundation Symposium Proceedings)” Book Review: This book talks about structural biology becoming a routine technique for structure determination in pharmaceutical industries. This book talks about the numerous initiatives in the field of “structural genomics” that are distributed all over the world. These have led to the development of techniques for high-throughput structure determina-tion. This structural information is being explored in various ways in the drug discovery process. This book also discusses the technique of structure-sequence compatibility (threading) that is increasingly used to assign a function to a given protein fold. This book will be useful for students and researchers in the field of structural biology.



2. Computational Structural Biology


1. “Computational Structural Biology: Methods and Applications” by Schwede Torsten

“Computational Structural Biology: Methods and Applications” Book Review: This book can be used as a guide for both students and practitioners. It provides a comprehensive overview of the major changes in the field of computational methods in structural biology. The book discusses the effect of computational methods with respect to protein structure and design. The book at the end of each chapter, other than the summary, the future of the field has been discussed, along with its challenges.

2. “Radiation Induced Molecular Phenomena in Nucleic Acids” by Manoj Shukla and Jerzy Leszczynski

“Radiation Induced Molecular Phenomena in Nucleic Acids: A Comprehensive Theoretical and Experimental Analysis (Challenges and Advances in Computational Chemistry and Physics (5) 2008th Edition” Book Review: This book strikes the balance between both theoretical and experimental knowledge for analysis of UV-radiation and low energy electron induced in NAB’s. The book highlights the plausible ways in which NAB’s can be worked with. The book also explores the technical challenges related to the field.

3. “Computational and Structural Approaches to Drug Discovery: Ligand-Protein Interactions (RSC Biomolecular Sciences)” by David M J Lilley and Amy S Anderson

“Computational and Structural Approaches to Drug Discovery: Ligand-Protein Interactions (RSC Biomolecular Sciences, Volume 8) 1st Edition” Book Review: This book is designed for all graduate level courses covering molecular interactions and drug discovery. It also provides references for the professionals in the pharmaceutical industry. The book highlights and explores both structural and chemical design of drug design. All factors necessary to encode, such as absorption, toxicology etc have been discussed. The book provides a detailed understanding of docking along with comparison and analysis of the methods and an insight into scoring algorithms.


4. “Molecular Structures and Structural Dynamics of Prion Proteins and Prions (Focus on Structural Biology)” by Jiapu Zhang - see Molecular Structures and Structural Dynamics of Prion Proteins and Prions | SpringerLink

“Molecular Structures and Structural Dynamics of Prion Proteins and Prions: Mechanism Underlying the Resistance to Prion Diseases (Focus on Structural Biology, 9) 2015 Edition” Book Review: This book is designed for practitioners in computing of biophysics, biochemistry, etc. This book is also a teaching material for students. It is the first book providing an easy and clear understanding of prion proteins’ molecular dynamics (MD) simulations and on prions’ molecular modelling (MM) constructions. Its design and effect is one crucial element discovered. The book is useful in understanding the mechanisms of prion diseases. Even though prions have no clear molecular structure, the unclear areas have been also explored in the text.

      



5. “Lecture Notes On Computational Structural Biology” by Zhijun Wu

“Lecture Notes on Computational Structural Biology” Book Review: This book aims to reduce the gap between the rapid developments in the field of structural bioinformatics. It is a collection of lecture notes, extensive research and the authors own knowledge about the subject field. It also provides content from the viewpoint of a computer scientist or applied mathematician. The book will help understand the importance of mathematics in this field.

6. “Bayesian Methods in Structural Bioinformatics (Statistics for Biology and Health)” by Thomas Hamelryck and Kanti Mardia

“Bayesian Methods in Structural Bioinformatics (Statistics for Biology and Health) 2012th Edition” Book Review: the book provides an overview of the current statistical methods used to solve problems in structural bioinformatics. It talks about statistical methods within the framework of statistical physics. The book deals with biomolecular structure in atomic details. The book begins with basic introduction and assumes minimum knowledge of proteins and mathematics.

7. “Structural Genomics and Drug Discovery (Methods in Molecular Biology)” by Wayne Anderson

“Structural Genomics and Drug Discovery: Methods and Protocols (Methods in Molecular Biology (1140)” Book Review: This book provides the methods and protocols for the discovery of structure of drugs. It provides all steps and tools required to canary out the procedures in a laboratory. The book also provides tips to avoid potential drawbacks.

8. “RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods (Methods in Molecular Biology)” by Jan Gorodkin and Walter L Ruzzo

“RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods (Methods in Molecular Biology (1097)) 2014th Edition” Book Review: Methodologies both computational and bioinformatics highlight both practical and computational/algorithmic perspectives in this field. RNA bioinformatics as well as related algorithms have been detailed. Chapters provide detailed description of topics with advice to obtain crucial results.

9. “Advance in Structural Bioinformatics (Advances in Experimental Medicine and Biology)” by Dongqing Wei and Qin Xu

“Advance in Structural Bioinformatics (Advances in Experimental Medicine and Biology (827)) 2015th Edition” Book Review: This book is designed for researchers and students in the fields of bioinformatics, computational biology and chemistry. The book details mathematical and physical modelling with the help of case studies and researches. The book provides information on structure bioinformatics at different levels. The chapters move from basics to the advanced. It also provides guidelines on acquiring and analyzing genomics and proteomics sequences, protein structures etc.

10. “Structural Bioinformatics” by Jenny Gu and Philip E Bourne

“Structural Bioinformatics 2nd Edition” Book Review: This book is designed for graduate and undergraduate university courses. The book provides the applications and the basic principles in the field of structural bioinformatics. The book is updated with newer developments in the field. The book includes topics such as sampling and search techniques; use of mass spectrometry etc.




References

[1] https://en.wikipedia.org/wiki/Russell_S._Drago Reference 4.  "Best Reference Books – Physical Methods in Inorganic Chemistry – Sanfoundry". 20 November 2013.

[2] https://www.sanfoundry.com/

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M.Sc. Mathematics


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Non Linear Programming


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Best Books – Non Linear Programming

  1. “Nonlinear Programming: Theory and Algorithms” by Hanif D Sherali & C M Shetty Mokhtar S Bazaraa

  2. “An Introduction to Nonlinear Optimization Theory” by Marius Durea and Radu Strugariu

  3. “Linear and Nonlinear Programming” by David G Luenberger and Yinyu Ye

  4. “Nonlinear Programming: Analysis and Methods (Dover Books on Computer Science)” by Mordecai Avriel

  5. “The Mathematics of Nonlinear Programming (Undergraduate Texts in Mathematics)” by Anthony L Peressini and Francis E Sullivan

  6. “Nonlinear Programming: Theory and Algorithms” by Mokhtar S Bazaraa and Hanif D Sherali

  7. “Nonlinear Programming: Concepts, Algorithms, and Applications to Chemical Processes (MPS-SIAM Series on Optimization)” by Lorenz T Biegler

  8. “Linear and Nonlinear Programming (International Series in Operations Research & Management Science)” by David G Luenberger and Yinyu Ye

  9. “Methods of Mathematical Economics: Linear and Nonlinear Programming, Fixed-Point Theorems (Undergraduate Texts in Mathematics)” by Joel N Franklin

  10. “Applied Nonlinear Programming” by Sanjay Sharma



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