Protein Geometry, Classification, Topology and Symmetry: A Computational Analysis of Structure (Series in Biophysics)

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Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure. The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

Power Laws, Scale-Free Networks and Genome Biology (Molecular Biology Intelligence Unit)

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Power Laws, Scale-Free Networks and Genome Biology (Molecular Biology Intelligence Unit)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0387258833

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Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for discovery of new biological phenomena.

Computational Biochemistry and Biophysics

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latest computational methods

Computational Biochemistry and Biophysics

Manufacturer: CRC
ProductGroup: Book
Binding: Hardcover

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ASIN: 082470455X

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Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.

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latest computational methods.......2004-12-31

This reference is a nice example of Moore's Law impinging on many fields. The falling cost of computation makes the book's techniques feasible as routine research tools.

Many types of methods are described. Such as solving systems of coupled nonlinear differential rate equations. Or applying free energy minimisation ideas from physics, to ever-larger molecular systems, to find their optimal shapes. This is illustrated with nice screen captures of the molecules.

The book indicates how computational chemistry has emerged as an intellectually viable branch of chemistry.

Advances in Chemical Physics, Computational Methods for Protein Folding (Advances in Chemical Physics)

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Advances in Chemical Physics, Computational Methods for Protein Folding (Advances in Chemical Physics)

Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471209554

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Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels.

Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies.

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The foundation for understanding the function and dynamics of biological systems is not only knowledge of their structure, but the new methodologies and applications used to determine that structure.

Electron magnetic resonance has been greatly facilitated by the introduction of advances in instrumentation and better computational tools, such as the increasingly widespread use of the density matrix formalism.

Computational and Instrumental Methods in EPR is devoted to both instrumentation and computation aspects of EPR, while addressing applications such as spin relaxation time measurements, the measurement of hyperfine interaction parameters, and the recovery of Mn(II) spin Hamiltonian parameters via spectral simulation.

Computational Methods for Protein Structure Prediction and Modeling 1: Basic Characterization (Biological and Medical Physics, Biomedical Engineering)

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Computational Methods for Protein Structure Prediction and Modeling 1: Basic Characterization (Biological and Medical Physics, Biomedical Engineering)

Manufacturer: Springer
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Binding: Hardcover

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ASIN: 0387333193

Book Description

Volume one of this two volume sequence focuses on the basic characterization of known protein structures as well as structure prediction from protein sequence information. The 11 chapters provide an overview of the field, covering key topics in modeling, force fields, classification, computational methods, and struture prediction. Each chapter is a self contained review designed to cover (1) definition of the problem and an historical perspective, (2) mathematical or computational formulation of the problem, (3) computational methods and algorithms, (4) performance results, (5) existing software packages, and (6) strengths, pitfalls, challenges, and future research directions.

Computational Methods for Protein Structure Prediction and Modeling 2: Structure Prediction (Biological and Medical Physics, Biomedical Engineering)

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Computational Methods for Protein Structure Prediction and Modeling 2: Structure Prediction (Biological and Medical Physics, Biomedical Engineering)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0387333215

Book Description

Volume two of this two volume sequence focuses on protein structure prediction and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.

From Physics to Biology: The Interface between Experiment and Computation: Bifi 2006 II International Congress (AIP Conference Proceedings)

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From Physics to Biology: The Interface between Experiment and Computation: Bifi 2006 II International Congress (AIP Conference Proceedings)

Manufacturer: American Institute of Physics
ProductGroup: Book
Binding: Hardcover

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Book Description

All papers in this volume were peer-reviewed. The BIFI2006 Conference represents an interactive forum for physicists, chemists, biologists, and mathematicians for sharing ideas as well as adressing recent advances in the frontier between physics and biology. Current challenges in molecular and cell biology, biomedicine, and biotechnology require the interdisciplinary collaborative effort of theoretical and experimental researchers benefiting from the interplay between the latest computational and experimental developments. There were three main topics at the conference: nucleic acids, proteins and peptides, and collective behavior of biomolecules. This volume includes papers on: protein folding, nucleic acid structure, ligand binding, proteomics, network dynamics and topology, cell signaling, collective behavior, biomolecular modeling, systems biology, and biophysical computational methods.

Multiple Aspects of DNA and RNA: from Biophysics to Bioinformatics, Volume Session LXXXII: Lecture Notes of the Les Houches Summer School 2004 (Les Houches)

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Multiple Aspects of DNA and RNA: from Biophysics to Bioinformatics, Volume Session LXXXII: Lecture Notes of the Les Houches Summer School 2004 (Les Houches)

Manufacturer: Elsevier Science
ProductGroup: Book
Binding: Hardcover

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ASIN: 0444520813

Book Description

This book is dedicated to the multiple aspects, that is, biological, physical and computational of DNA and RNA molecules. These molecules, central to vital processes, have been experimentally studied by molecular biologists for five decades since the discovery of the structure of DNA by Watson and Crick in 1953. Recent progresses (e.g. use of DNA chips, manipulations at the single molecule level, availability of huge genomic databases...) have revealed an imperious need for theoretical modelling. Further progresses will clearly not be possible without an integrated understanding of all DNA and RNA aspects and studies.

The book is intended to be a desktop reference for advanced graduate students or young researchers willing to acquire a broad interdisciplinary understanding of the multiple aspects of DNA and RNA. It is divided in three main sections:

The first section comprises an introduction to biochemistry and biology of nucleic acids. The structure and function of DNA are reviewed in R. Lavery's chapter. The next contribution, by V. Fritsch and E. Westhof, concentrates on the folding properties of RNA molecules. The cellular processes involving these molecules are reviewed by J. Kadonaga, with special emphasis on the regulation of transcription. These chapters does not require any preliminary knowledge in the field (except that of elementary biology and chemistry).

The second section covers the biophysics of DNA and RNA, starting with basics in polymer physics in the contribution by R. Khokhlov. A large space is then devoted to the presentation of recent experimental and theoretical progresses in the field of single molecule studies. T. Strick's contribution presents a detailed description of the various micro-manipulation techniques, and reviews recent experiments on the interactions between DNA and proteins (helicases, topoisomerases, ...). The theoretical modeling of single molecules is presented by J. Marko, with a special attention paid to the elastic and topological properties of DNA. Finally, advances in the understanding of electrophoresis, a technique of crucial importance in everyday molecular biology, are exposed in T. Duke's contribution.

The third section presents provides an overview of the main computational approaches to integrate, analyse and simulate molecular and genetic networks. First, J. van Helden introduces a series of statistical and computational methods allowing the identification of short nucleic fragments putatively involved in the regulation of gene expression from sets of promoter sequences controlling co-expressed genes. Next, the chapter by Samsonova et al. connects this issue of transcriptional regulation with that of the control of cell differentiation and pattern formation during embryonic development. Finally, H. de Jong and D. Thieffry review a series of mathematical approaches to model the dynamical behaviour of complex genetic regulatory networks. This contribution includes brief descriptions and references to successful applications of these approaches, including the work of B. Novak, on the dynamical modelling of cell cycle in different model organisms, from yeast to mammals.

. Provides a comprehensive overview of the structure and function of DNA and RNA at the interface between physics, biology and information science.

Book Description

Speciation is the process by which co-existing daughter species evolve from one ancestral species - e.g., humans, chimpanzees, and gorillas arising from a common ancestor around 5,000,000 years ago. However, many questions about speciation remain controversial. The Birds of Northern Melanesia provides by far the most comprehensive study yet available of a rich fauna, composed of the 195 breeding land and fresh-water bird species of the Bismarck and Solomon Archipelagoes east of New Guinea. This avifauna offers decisive advantages for understanding speciation, and includes famous examples of geographic variation discussed in textbooks of evolutionary biology. The book results from 30 years of collaboration between the evolutionary biologist Ernst Mayr and the ecologist Jared Diamond. It shows how Northern Melanesian bird distributions provide snapshots of all stages in speciation, from the earliest (widely distributed species without geographic variation) to the last (closely related, reproductively isolated species occurring sympatrically and segregating ecologically). The presentation emphasizes the wide diversity of speciation outcomes, steering a middle course between one-model-fits-all simplification and ungeneralizable species accounts. Questions illuminated include why some species are much more prone to speciate than others, why some water barriers are much more effective at promoting speciation than others, and whether hypothesized taxon cycles, faunal dominance, and legacies of Pleistocene land bridges are real. These years of study have resulted in a huge database, complete with distributions of all 195 species on 76 islands, together with their taxonomy, colonization routes, ecological attributes, abundance, and overwater dispersal. Color plates depict 88 species and allospecies, many of which have never been seen before. For students of speciation, Northern Melanesian birds now constitute a model system against which other biotas can be compared. For population biologists interested in other problems besides speciation, this rich database can now be mined for insights.

Speciation specifics. (Scientists Bookshelf).: An article from: American Scientist

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Speciation specifics. (Scientists Bookshelf).: An article from: American Scientist

Manufacturer: Sigma Xi, The Scientific Research Society
ProductGroup: Book
Binding: Digital

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The Birds of Northern Melanesia: Speciation, Ecology, and Biogeography

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The Birds of Northern Melanesia: Speciation, Ecology, and Biogeography
Ernst Mayr; Jared Diamond
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback
ASIN: B000OKNLWK

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