Entropy And Free Energy In Structural Biology

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Entropy and Free Energy in Structural Biology

Hagai Meirovitch
Entropy and Free Energy in Structural Biology Book PDF

Author : Hagai Meirovitch
Publisher : CRC Press
Page : 374 pages
File Size : 42,5 Mb
Release : 2020-08-14
Category : Computers
ISBN : 9781000072303

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Entropy and Free Energy in Structural Biology by Hagai Meirovitch Pdf

Computer simulation has become the main engine of development in statistical mechanics. In structural biology, computer simulation constitutes the main theoretical tool for structure determination of proteins and for calculation of the free energy of binding, which are important in drug design. Entropy and Free Energy in Structural Biology leads the reader to the simulation technology in a systematic way. The book, which is structured as a course, consists of four parts: Part I is a short course on probability theory emphasizing (1) the distinction between the notions of experimental probability, probability space, and the experimental probability on a computer, and (2) elaborating on the mathematical structure of product spaces. These concepts are essential for solving probability problems and devising simulation methods, in particular for calculating the entropy. Part II starts with a short review of classical thermodynamics from which a non-traditional derivation of statistical mechanics is devised. Theoretical aspects of statistical mechanics are reviewed extensively. Part III covers several topics in non-equilibrium thermodynamics and statistical mechanics close to equilibrium, such as Onsager relations, the two Fick's laws, and the Langevin and master equations. The Monte Carlo and molecular dynamics procedures are discussed as well. Part IV presents advanced simulation methods for polymers and protein systems, including techniques for conformational search and for calculating the potential of mean force and the chemical potential. Thermodynamic integration, methods for calculating the absolute entropy, and methodologies for calculating the absolute free energy of binding are evaluated. Enhanced by a number of solved problems and examples, this volume will be a valuable resource to advanced undergraduate and graduate students in chemistry, chemical engineering, biochemistry biophysics, pharmacology, and computational biology.

Fundamentals of Molecular Structural Biology

Subrata Pal
Fundamentals of Molecular Structural Biology Book PDF

Author : Subrata Pal
Publisher : Academic Press
Page : 518 pages
File Size : 42,7 Mb
Release : 2019-08-13
Category : Science
ISBN : 9780128148563

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Fundamentals of Molecular Structural Biology by Subrata Pal Pdf

Fundamentals of Molecular Structural Biology reviews the mathematical and physical foundations of molecular structural biology. Based on these fundamental concepts, it then describes molecular structure and explains basic genetic mechanisms. Given the increasingly interdisciplinary nature of research, early career researchers and those shifting into an adjacent field often require a "fundamentals" book to get them up-to-speed on the foundations of a particular field. This book fills that niche. Provides a current and easily digestible resource on molecular structural biology, discussing both foundations and the latest advances Addresses critical issues surrounding macromolecular structures, such as structure-based drug discovery, single-particle analysis, computational molecular biology/molecular dynamic simulation, cell signaling and immune response, macromolecular assemblies, and systems biology Presents discussions that ultimately lead the reader toward a more detailed understanding of the basis and origin of disease

Thermodynamics in Biology

Enrico Di Cera
Thermodynamics in Biology Book PDF

Author : Enrico Di Cera
Publisher : Oxford University Press, USA
Page : 250 pages
File Size : 50,5 Mb
Release : 2000
Category : Medical
ISBN : 0195123271

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Thermodynamics in Biology by Enrico Di Cera Pdf

Enrico Di Cera, a rising star in biophysics, has organized a superb group of authors to write substantial chapters covering the most exciting and central issues relating to the bioenergetic aspects of proteins, nucleic acids, and their interactions. Topics covered in this book are protein and nucleic acid folding and stability, enzyme-substrate interactions, prediction of the affinity of complexes, electrostatics, and non-equilibrium aspects of protein function. The breadth of the topics covered in this book illustrates the growing importance of thermodynamic approaches in the study of biological phenomena. The book should be of wide interest to biophysicists, biochemists, and structural biologists.

Advances in Protein Molecular and Structural Biology Methods

Timir Tripathi,Vikash Kumar Dubey
Advances in Protein Molecular and Structural Biology Methods Book PDF

Author : Timir Tripathi,Vikash Kumar Dubey
Publisher : Academic Press
Page : 716 pages
File Size : 46,6 Mb
Release : 2022-01-14
Category : Science
ISBN : 9780323902656

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Advances in Protein Molecular and Structural Biology Methods by Timir Tripathi,Vikash Kumar Dubey Pdf

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

Mass Spectrometry in Structural Biology and Biophysics

Igor A. Kaltashov,Stephen J. Eyles
Mass Spectrometry in Structural Biology and Biophysics Book PDF

Author : Igor A. Kaltashov,Stephen J. Eyles
Publisher : John Wiley & Sons
Page : 312 pages
File Size : 49,6 Mb
Release : 2012-04-03
Category : Science
ISBN : 9780470937792

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Mass Spectrometry in Structural Biology and Biophysics by Igor A. Kaltashov,Stephen J. Eyles Pdf

The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.

Foundations of Bioenergetics

Harold Morowitz
Foundations of Bioenergetics Book PDF

Author : Harold Morowitz
Publisher : Elsevier
Page : 364 pages
File Size : 40,7 Mb
Release : 2012-12-02
Category : Science
ISBN : 9780323154055

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Foundations of Bioenergetics by Harold Morowitz Pdf

Foundations of Bioenergetics provides an introduction to the physical foundations of bioenergetics and the methods of applying these constructs to biological problems. It combines parts of thermal physics, biochemistry, ecology, and cellular and organismic biology into a single coherent work. Much of the material in this volume comes from ""Entropy for Biologists,"" an introductory thermodynamics book aimed particularly at life scientists. Some of the topics originally appeared in the monograph ""Energy Flow in Biology."" The current volume expands on that material with respect to biological applications and attempts to bridge the gap between physics and biology. The book explains basic concepts such as energy, temperature, the second law of thermodynamics, entropy, information theory, and statistical mechanics. It discusses the relations between thermodynamics and statistical mechanics, free-energy functions, radiant energy, the free energy of cells and tissue, chemical kinetics, and cyclic flows. It examines the relationships between energy flows and biological processes; applications of the concepts of Gibbs free energy, chemical potential, and activity; and measurements of temperature, energy, and thermochemical quantities. The book also includes chapters that deal with irreversible dynamics, irreversible theory, and osmotic flow.

Entropy for Biologists

Harold J. Morowitz
Entropy for Biologists Book PDF

Author : Harold J. Morowitz
Publisher : Elsevier
Page : 212 pages
File Size : 54,8 Mb
Release : 2013-09-03
Category : Science
ISBN : 9781483263168

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Entropy for Biologists by Harold J. Morowitz Pdf

Entropy for Biologists: An Introduction to Thermodynamics is an introductory book for people in the life sciences who wish to master the concepts of thermal physics without being forced to a degree and rate of symbol manipulation which is foreign to their patterns of thought. The book opens with a chapter on temperature, followed by separate chapters that discuss the concepts of energy, kinetic theory, total energy, the second law of thermodynamics, entropy, and probability and information theory. Subsequent chapters deal with statistical mechanics and its relation to thermodynamics, free-energy functions, applications of the Gibbs free energy and the Gibbs chemical potential, and measurement in thermal physics. The book is primarily directed at those graduate and advanced undergraduate students of biology and biochemistry who wish to develop a sense of confidence about their understanding of the thermal physics which will be useful in pursuing their work. It may also prove useful to professionals who wish to bolster their knowledge in this area.

Advances in Protein and Peptide Sciences

Ben M. Dunn
Advances in Protein and Peptide Sciences Book PDF

Author : Ben M. Dunn
Publisher : Bentham Science Publishers
Page : 911 pages
File Size : 52,8 Mb
Release : 2013-10-30
Category : Science
ISBN : 9781608054879

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Advances in Protein and Peptide Sciences by Ben M. Dunn Pdf

Advances in Protein and Peptide Sciences is a book series focused on leading-edge research on the structure, physical properties, and functions of proteins and peptides. The series presents highly cited contributions first published in the journal Current Protein and Peptide Science. Authors of these contributions have updated their work with new experimental data and references following their initial research. Each volume highlights a number of important topics in current research in the field of protein and peptide chemistry and molecular biology, including membrane proteins and their interactions with ligands, computational methods, and proteins in disease and biotechnology.

Lecture Notes on Computational Structural Biology

Zhijun Wu
Lecture Notes on Computational Structural Biology Book PDF

Author : Zhijun Wu
Publisher : World Scientific
Page : 243 pages
File Size : 40,9 Mb
Release : 2008
Category : Science
ISBN : 9789812814784

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Lecture Notes on Computational Structural Biology by Zhijun Wu Pdf

1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond

Dynamics and Kinetics in Structural Biology

Keith Moffat,Eaton E. Lattman
Dynamics and Kinetics in Structural Biology Book PDF

Author : Keith Moffat,Eaton E. Lattman
Publisher : John Wiley & Sons
Page : 292 pages
File Size : 41,8 Mb
Release : 2024-01-03
Category : Science
ISBN : 9781119696285

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Dynamics and Kinetics in Structural Biology by Keith Moffat,Eaton E. Lattman Pdf

Understand the latest experimental tools in structural biology with this pioneering work Structural biology seeks to understand the chemical mechanisms and functions of biological molecules, such as proteins, based on their atomic structures. Until recently, these structures have been studied only statically, using procedures which deliberately freeze atomic motion. However, freezing eliminates the rapid structural motions so essential to biological activity and function; the molecules are inactive. But with the recent development of X-ray free electron laser (XFEL) sources, efforts to conduct dynamic experiments have expanded using the principles of dynamics and kinetics to capture active biological molecules as they function. Dynamics and Kinetics in Structural Biology promotes the development of these experiments and their successful application. It grounds readers in the foundational principles of dynamics and kinetics; proceeds through extended discussions of experimental procedures, data analysis techniques; and explores experimental frontiers in structural dynamics. The book will aid researchers to gather and interpret cutting-edge data on the dynamic structure of biological molecules, under conditions where they retain their biological functions. Dynamics and Kinetics in Structural Biology offers readers: Authorship by founding figures in the field In-depth presentation of time-resolved X-ray crystallography, solution scattering, and more A pioneering contribution to a rapidly developing field of study Dynamics and Kinetics in Structural Biology is essential reading for graduate students, scientists, researchers and industry professionals engaged in structural studies of biological systems. Industry professionals considering dynamic studies in the development of new product lines will also benefit.

Computational Chemistry Methods in Structural Biology

Christo Christov
Computational Chemistry Methods in Structural Biology Book PDF

Author : Christo Christov
Publisher : Academic Press
Page : 360 pages
File Size : 45,8 Mb
Release : 2011-09-23
Category : Science
ISBN : 9780123864857

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Computational Chemistry Methods in Structural Biology by Christo Christov Pdf

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. Essential resource for protein chemists This volume features articles on Computational Chemistry methods in Structural Biology

Structural Biology in Drug Discovery

Jean-Paul Renaud
Structural Biology in Drug Discovery Book PDF

Author : Jean-Paul Renaud
Publisher : John Wiley & Sons
Page : 688 pages
File Size : 53,6 Mb
Release : 2020-01-27
Category : Medical
ISBN : 9781118900406

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Structural Biology in Drug Discovery by Jean-Paul Renaud Pdf

With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins

Algorithms in Structural Molecular Biology

Bruce R. Donald
Algorithms in Structural Molecular Biology Book PDF

Author : Bruce R. Donald
Publisher : MIT Press
Page : 497 pages
File Size : 43,8 Mb
Release : 2023-08-15
Category : Science
ISBN : 9780262548793

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Algorithms in Structural Molecular Biology by Bruce R. Donald Pdf

An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Biology for AP ® Courses

Julianne Zedalis,John Eggebrecht
Biology for AP Courses Book PDF

Author : Julianne Zedalis,John Eggebrecht
Publisher : Unknown
Page : 1923 pages
File Size : 53,8 Mb
Release : 2017-10-16
Category : Biology
ISBN : 1947172409

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Biology for AP ® Courses by Julianne Zedalis,John Eggebrecht Pdf

Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.

Research in Computational Molecular Biology

Terence Terry Speed,Haiyan Huang
Research in Computational Molecular Biology Book PDF

Author : Terence Terry Speed,Haiyan Huang
Publisher : Springer Science & Business Media
Page : 565 pages
File Size : 47,5 Mb
Release : 2007-04-05
Category : Science
ISBN : 9783540716808

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Research in Computational Molecular Biology by Terence Terry Speed,Haiyan Huang Pdf

This book constitutes the refereed proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007, held in Oakland, CA, USA in April 2007. The 37 revised full papers address all current issues in algorithmic, theoretical, and experimental bioinformatics.