Integrative Structural Biology with Hybrid Methods

Integrative Structural Biology with Hybrid Methods

Author: Haruki Nakamura

Publisher: Springer

Published: 2019-01-08

Total Pages: 270

ISBN-13: 9811322007

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This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.


Opportunities in Biology

Opportunities in Biology

Author: National Research Council

Publisher: National Academies

Published: 1989-01-01

Total Pages: 471

ISBN-13: 0309039274

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Biology has entered an era in which interdisciplinary cooperation is at an all-time high, practical applications follow basic discoveries more quickly than ever before, and new technologiesâ€"recombinant DNA, scanning tunneling microscopes, and moreâ€"are revolutionizing the way science is conducted. The potential for scientific breakthroughs with significant implications for society has never been greater. Opportunities in Biology reports on the state of the new biology, taking a detailed look at the disciplines of biology; examining the advances made in medicine, agriculture, and other fields; and pointing out promising research opportunities. Authored by an expert panel representing a variety of viewpoints, this volume also offers recommendations on how to meet the infrastructure needsâ€"for funding, effective information systems, and other supportâ€"of future biology research. Exploring what has been accomplished and what is on the horizon, Opportunities in Biology is an indispensable resource for students, teachers, and researchers in all subdisciplines of biology as well as for research administrators and those in funding agencies.


Biomolecular Structure and Dynamics

Biomolecular Structure and Dynamics

Author: G. Vergoten

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 327

ISBN-13: 9401154848

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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.


Concepts and Experimental Protocols of Modelling and Informatics in Drug Design

Concepts and Experimental Protocols of Modelling and Informatics in Drug Design

Author: Om Silakari

Publisher: Academic Press

Published: 2020-11-05

Total Pages: 398

ISBN-13: 0128205474

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Concepts and Experimental Protocols of Modelling and Informatics in Drug Design discusses each experimental protocol utilized in the field of bioinformatics, focusing especially on computer modeling for drug development. It helps the user in understanding the field of computer-aided molecular modeling (CAMM) by presenting solved exercises and examples. The book discusses topics such as fundamentals of molecular modeling, QSAR model generation, protein databases and how to use them to select and analyze protein structure, and pharmacophore modeling for drug targets. Additionally, it discusses data retrieval system, molecular surfaces, and freeware and online servers. The book is a valuable source for graduate students and researchers on bioinformatics, molecular modeling, biotechnology and several members of biomedical field who need to understand more about computer-aided molecular modeling. - Presents exercises with solutions to aid readers in validating their own protocol - Brings a thorough interpretation of results of each exercise to help readers compare them to their own study - Explains each parameter utilized in the algorithms to help readers understand and manipulate various features of molecules and target protein to design their study


Computational Modeling of Biological Systems

Computational Modeling of Biological Systems

Author: Nikolay V Dokholyan

Publisher: Springer Science & Business Media

Published: 2012-02-12

Total Pages: 360

ISBN-13: 1461421454

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Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.


Molecular Modeling and Simulation

Molecular Modeling and Simulation

Author: Tamar Schlick

Publisher: Springer Science & Business Media

Published: 2013-04-18

Total Pages: 669

ISBN-13: 0387224645

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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text


Protein Conformational Dynamics

Protein Conformational Dynamics

Author: Ke-li Han

Publisher: Springer Science & Business Media

Published: 2014-01-20

Total Pages: 488

ISBN-13: 3319029703

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This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.