Journal of biomolecular structure & dynamics


Book Description

Presents information about the "Journal of Biomolecular Structure and Dynamics" (JBSD), published by Adenine Press, located in Schenectady, New York. Lists the editor-in-chief and the board of editors. Notes that the periodical (ISSN 0739-1102), is published bimonthly and covers both experimental and theoretical investigations in the areas of biological structure, dynamics, interaction, and expression. Offers access to the cover page, a table of contents, and abstracts from the articles of the print version. Contains submission instructions for prospective authors. Includes subscription information. Posts contact information for the editor-in-chief via mailing address, telephone and fax numbers, and e-mail.







Biomolecular Structure and Dynamics


Book Description

Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.







Macromolecular Crystallography


Book Description

This volume is a collection of the contributions presented at the 42nd Erice Crystallographic Course whose main objective was to train the younger generation on advanced methods and techniques for examining structural and dynamic aspects of biological macromolecules. The papers review the techniques used to study protein assemblies and their dynamics, including X-ray diffraction and scattering, electron cryo-electron microscopy, electro nanospray mass spectrometry, NMR, protein docking and molecular dynamics. A key theme throughout the book is the dependence of modern structural science on multiple experimental and computational techniques, and it is the development of these techniques and their integration that will take us forward in the future.




Chemical Reactivity Theory


Book Description

In the 1970s, Density Functional Theory (DFT) was borrowed from physics and adapted to chemistry by a handful of visionaries. Now chemical DFT is a diverse and rapidly growing field, its progress fueled by numerous developing practical descriptors that make DFT as useful as it is vast. With 34 chapters written by 65 eminent scientists from 13 diffe




Biomolecular Simulations


Book Description

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.




Dynamics of Proteins and Nucleic Acids


Book Description

This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.




Mass Spectrometry in Biophysics


Book Description

The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.




Ab Initio Molecular Dynamics


Book Description

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.