computational and visualization techniques for structural bioinformatics using chimera chapman hall crc mathematical and computational biology

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Computational And Visualization Techniques For Structural Bioinformatics Using Chimera

Author : Forbes J. Burkowski
ISBN : 9781439836620
Genre : Science
File Size : 86. 96 MB
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A Step-by-Step Guide to Describing Biomolecular Structure Computational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation. Understand Important Concepts of Structural Bioinformatics The book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website. Build Python Scripts to Extend the Capabilities of Chimera Through more than 60 exercises that involve the development of Python scripts, the book gives you concrete guidance on using the scripting capabilities of Chimera. You’ll gain experience in solving real problems as well as understand the various applications of linear algebra. You can also use the scripts as starting points for the development of similar applications and use classes from the StructBio toolkit for computations, such as structure overlap, data plotting, scenographics, and display of residue networks.

Chromatin

Author : Ralf Blossey
ISBN : 9781351646819
Genre : Medical
File Size : 54. 34 MB
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An invaluable resource for computational biologists and researchers from other fields seeking an introduction to the topic, Chromatin: Structure, Dynamics, Regulation offers comprehensive coverage of this dynamic interdisciplinary field, from the basics to the latest research. Computational methods from statistical physics and bioinformatics are detailed whenever possible without lengthy recourse to specialized techniques.

The Pyrosetta Interactive Platform For Protein Structure Prediction And Design

Author : Jeffrey J. Gray
ISBN : 1542402131
Genre :
File Size : 22. 55 MB
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PyRosetta4 UPDATE (2017) INCLUDED ... This book contains a set of workshops which teach the PyRosetta program for computational protein structure prediction and design. PyRosetta (http: //www.pyrosetta.org) is a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite. Rosetta, developed by a consortium of laboratories in the Rosetta Commons, has an unmatched variety of functionalities and is one of the most accurate protein structure prediction and design approaches. The workshops teach how to measure and manipulate protein conformations, calculate energies in low- and high-resolution representations, fold proteins from sequence, model variable regions of proteins (loops), dock proteins or small molecules, design protein sequences, and build custom protocols for operations tailored to particular biomolecular applications

Introduction To Proteins

Author : Amit Kessel
ISBN : 1498747175
Genre : Medical
File Size : 59. 22 MB
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Introduction to Proteins shows how proteins can be analyzed in multiple ways. It refers to the roles of proteins and enzymes in diverse contexts and everyday applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. This edition includes a brand-new chapter on enzymatic catalysis and biochemistry, an in-depth discussion of G-protein-coupled receptors (GPCRs), and a wider-scale description of methods for studying proteins.

Computational Biology

Author : Ralf Blossey
ISBN : 1584885564
Genre : Science
File Size : 60. 92 MB
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Quantitative methods have a particular knack for improving any field they touch. For biology, computational techniques have led to enormous strides in our understanding of biological systems, but there is still vast territory to cover. Statistical physics especially holds great potential for elucidating the structural-functional relationships in biomolecules, as well as their static and dynamic properties. Breaking New Ground Computational Biology: A Statistical Mechanics Perspective is the first book dedicated to the interface between statistical physics and bioinformatics. Introducing both equilibrium and nonequilibrium statistical mechanics in a manner tailored to computational biologists, the author applies these methods to understand and model the properties of various biomolecules and biological networks at the systems level. Unique Vision, Novel Approach Blossey combines his enthusiasm for uniting the fields of physics and computational biology with his considerable experience, knowledge, and gift for teaching. He uses numerous examples and tasks to illustrate and test understanding of the concepts, and he supplies a detailed keyword list for easy navigation and comprehension. His approach takes full advantage of the latest tools in statistical physics and computer science to build a strong set of tools for confronting new challenges in computational biology. Making the concepts crystal clear without sacrificing mathematical rigor, Computational Biology: A Statistical Mechanics Perspective is the perfect tool to broaden your skills in computational biology.

Practical Bioinformatics

Author : Janusz M. Bujnicki
ISBN : 9783540742685
Genre : Science
File Size : 55. 70 MB
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This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.

Computational Exome And Genome Analysis

Author : Peter N. Robinson
ISBN : 9781351650816
Genre : Mathematics
File Size : 56. 61 MB
Format : PDF, ePub
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Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Structural Bioinformatics

Author : Forbes J. Burkowski
ISBN : 9781420011791
Genre : Science
File Size : 53. 77 MB
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The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing 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 Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).

Introduction To Mathematical Oncology

Author : Yang Kuang
ISBN : 9781584889915
Genre : Mathematics
File Size : 68. 82 MB
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Introduction to Mathematical Oncology presents biologically well-motivated and mathematically tractable models that facilitate both a deep understanding of cancer biology and better cancer treatment designs. It covers the medical and biological background of the diseases, modeling issues, and existing methods and their limitations. The authors introduce mathematical and programming tools, along with analytical and numerical studies of the models. They also develop new mathematical tools and look to future improvements on dynamical models. After introducing the general theory of medicine and exploring how mathematics can be essential in its understanding, the text describes well-known, practical, and insightful mathematical models of avascular tumor growth and mathematically tractable treatment models based on ordinary differential equations. It continues the topic of avascular tumor growth in the context of partial differential equation models by incorporating the spatial structure and physiological structure, such as cell size. The book then focuses on the recent active multi-scale modeling efforts on prostate cancer growth and treatment dynamics. It also examines more mechanistically formulated models, including cell quota-based population growth models, with applications to real tumors and validation using clinical data. The remainder of the text presents abundant additional historical, biological, and medical background materials for advanced and specific treatment modeling efforts. Extensively classroom-tested in undergraduate and graduate courses, this self-contained book allows instructors to emphasize specific topics relevant to clinical cancer biology and treatment. It can be used in a variety of ways, including a single-semester undergraduate course, a more ambitious graduate course, or a full-year sequence on mathematical oncology.

Structural Bioinformatics

Author : Jenny Gu
ISBN : 9781118210567
Genre : Science
File Size : 89. 55 MB
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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

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