Structural Bioinformatics (Methods of Biochemical Analysis, V. 44)

Book Description

From the Foreword
"[A] must read for all of us committed to understanding the interplay of structure and function...[T]he individual chapters outline the suite of major basic life science questions such as the status of efforts to predict protein structure and how proteins carry out cellular functions, and also the applied life science questions such as how structural bioinformatics can improve health care through accelerating drug discovery."

This book provides a basic understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics. The reader emerges with the ability to make effective use of protein, DNA, RNA, carbohydrate, and complex structures to better understand biological function. Moreover, it draws a clear connection between structural studies and the rational design of new therapies.

Customer Reviews:

A Legit review from a REAL: reader.......2006-06-16

Ok, there are 3 reviews listed here from what seems to be the authors or their closest friends... I give these about as much credit as whale dung at the bottom of the ocean. That being said, this *IS* an awesome summation of current knowledge in the fields of Structural biology and bioinformatics, especially for one with a working (undergraduate) knowledge of biological building blocks.
A few things of note: the book is aimed at biologists. This is not to imply that computer scientists or actuarial scientists will never understand this book, but rather implies that the approach to instruction is taken from the biological realm and then expanded to other related fields.
Also note that this is aimed strictly at comparative structural bioinformatics. While mentioned in the book, topics like transcription factors, x-ray crystalographic methods, or multi-cell signalling networks are best left for other books. This particular book, while touching on the subjects, does not go into much depth in these subjects. Personally, I feel this is all the better, allowing for a better primer of the subjects.
All in all, I have to say that this is one of the best books to date for an upper-undergraduate / graduate student to gain a working knowledge of Structural Bioinformatics. As such, I gladly rate this a 5 star book!

Terrific Book.......2003-10-17

"...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." (Briefings in Bioinformatics)

Useful and Timely.......2003-09-03

"...a useful and timely summary of a rapidly expanding field." (Nature Structural Biology, Vol. 10, No. 8, August 2003)

Recommended Book.......2003-07-25

"...recommended for anyone who wishes to develop bioinformatics tools for protein structure analysis." (The Biotech Journal, April/May 2003)

Solving Ordinary Differential Equations II: Stiff and Differential-Algebraic Problems (Springer Series in Computational Mathematics)

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Solving Ordinary Differential Equations II: Stiff and Differential-Algebraic Problems (Springer Series in Computational Mathematics)
Ernst Hairer , and Gerhard Wanner
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540604529

Book Description

The subject of this book is the solution of stiff differential equations and of differential-algebraic systems (differential equations with constraints). The book is divided into four chapters. The beginning of each chapter is of introductory nature, followed by practical applications, the discussion of numerical results, theoretical investigations on the order and accuracy, linear and nonlinear stability, convergence and asymptotic expansions. Stiff and differential-algebraic problems arise everywhere in scientific computations (e.g., in physics, chemistry, biology, control engineering, electrical network analysis, mechanical systems). Many applications as well as computer programs are presented.

Electronic Structure Calculations for Solids and Molecules: Theory and Computational Methods

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Electronic Structure Calculations for Solids and Molecules: Theory and Computational Methods
Jorge Kohanoff
Manufacturer: Cambridge University Press
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Binding: Hardcover

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ASIN: 0521815916

Book Description

Electronic structure problems are studied in condensed matter physics and theoretical chemistry to provide important insights into the properties of matter. This graduate textbook describes the main theoretical approaches and computational techniques, from the simplest approximations to the most sophisticated methods. It starts with a detailed description of the various theoretical approaches to calculating the electronic structure of solids and molecules, including density-functional theory and chemical methods based on Hartree-Fock theory. The basic approximations are thoroughly discussed, and an in-depth overview of recent advances and alternative approaches in DFT is given. The second part discusses the different practical methods used to solve the electronic structure problem computationally, for both DFT and Hartree-Fock approaches. Adopting a unique and open approach, this textbook is aimed at graduate students in physics and chemistry, and is intended to improve communication between these communities. It also serves as a reference for researchers entering the field.

High Content Screening (Methods in Molecular Biology)

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High Content Screening (Methods in Molecular Biology)

Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 1588297314

Book Description

High content screening (HCS) was developed by Cellomics Inc. in the mid-1990s to address the need for a platform that could be used in the discovery-driven research and development required to understand the functions of genes and gene products at the level of the cell. High Content Screening: A Powerful Approach to Systems Cell Biology and Drug Discovery discusses its use as a high throughput platform to understand the functions of genes, RNA, proteins, and other cellular constituents at the level of the living cell.
High Content Screening is assembled to assist both existing users of HCS, as well as investigators considering the addition of a discovery-driven platform to their research and development activities. The chapters have been organized into sections that highlight the importance of integrating instrumentation, application software, reagents, and informatics. In addition, there is a combination of pure review chapters on key topics and specific methods chapters.
Written by a team of world leaders in the field, High Content Screening is essential reading for senior scientists, advanced lab technicians, as well as students/post-docs who wish to apply HCS in their research and development programs.

Computational Methods in Physics, Chemistry and Biology: An Introduction

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Computational Methods in Physics, Chemistry and Biology: An Introduction
Paul Harrison
Manufacturer: Wiley
ProductGroup: Book
Binding: Paperback

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Computational Physics: An Introduction

ASIN: 0471495638

Book Description

Providing an accessible introduction to a range of modern computational techniques, this book is perfect for anyone with only a limited knowledge of physics. It leads readers through a series of examples, problems, and practical-based tasks covering the basics to more complex ideas and techniques. The focus is placed on the dynamic area
of modern physics, helping readers understand the power and uses of computational physics.

Leads the reader from a basic introduction to more sophisticated techniques
Provides the skill-building exercises necessary to tackle more complex problems
Applies essential techniques to a wide range of key problems

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Intersting Studies Hampered by LEDA and LP Dependencies

Algorithms on Trees and Graphs
Gabriel Valiente
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540435506

Book Description

Graph algorithms is a well-established subject in mathematics and computer science. Beyond classical application fields, like approximation, combinatorial optimization, graphics, and operations research, graph algorithms have recently attracted increased attention from computational molecular biology and computational chemistry. Centered around the fundamental issue of graph isomorphism, this text goes beyond classical graph problems of shortest paths, spanning trees, flows in networks, and matchings in bipartite graphs. Advanced algorithmic results and techniques of practical relevance are presented in a coherent and consolidated way. This book introduces graph algorithms on an intuitive basis followed by a detailed exposition in a literate programming style, with correctness proofs as well as worst-case analyses. Furthermore, full C++ implementations of all algorithms presented are given using the LEDA library of efficient data structures and algorithms. Numerous illustrations, examples, and exercises, and a comprehensive bibliography support students and professionals in using the book as a text and source of reference

Customer Reviews:

Intersting Studies Hampered by LEDA and LP Dependencies.......2003-12-24

I'm pleased with the text in this book; the descriptions are almost all clear, and reading through the book gives me insight into some more interesting problems in trees and graphs. The high points of the book are its treaments of tree and graph isomorphism, but I also found the discussions of non-traditional traversal algorithms on trees and graphs very interesting. The author discussions leaf-first, breadth-first, and depth-first traversals and provides algorithms for their implementation. Many of the algorithms include correctness proofs.

These topics alone made the book worth its to me. A deep academic book that costs less than $50 is nearly unheared-of.

Unfortunately, there are two flaws that make the book hard to use. In a nutshell, the author expects the reader to buy into a couple of pretty invasive and expensive propositions.

First, the author decided to use literate programming for all of his presented algorithms and code fragments. This isn't so bad, since literate programming is about documenting code. If you suppose that the author wrote the code, then documented it, then calld it a book, using a tool like literate programming seems like a natural choice.

But if you're not familiar with literate programming, it's a bit of a chore. The author's introduction to literate programming doesn't help with some of the questions even an experienced programmer might have wend reading the text. More practically, literate programming enforces operators that are different than most C/C++ developers are familiar with, and can cause confusion when reading the text. ^ is used, for example, to indicate a logical and, where C/C++ developers expect it to indicate a bitwise-exclusive or.

While it's esay to eventually overcome such tricks of memory, I've been finding it hard to scan literate programs to find definitions and declarations. The author doesn't include a CD (and at this cover price, that is hard to fault) but also doesn't make his code available for download. His website includes a LEDA-based program that interactively demonstrates some algorithms, but doesn't include code for the algorithm his own books develops and discusses.

The other decision made by the author, to the overwhelming inconvenience of this reader, is the reliance on the LEDA library for his samples and programs. The algorithms are understandable without the library, but a reader without access to LEDA doesn't benefit from any of the visualizations the author provides. , and several include

In fact, the author spends about 40 pages discussing LEDA and the characteristics of its implementation. Maybe researchers working on tree and graph algorithms all use LEDA and have ready access to it, but the literate programming code provided to for some of the algorithms isn't useful to readers who aren't familiar with LEDA, as researching the definitions and declarations themsleves becomes arduous.

The bibliography is very diverse, with more than 380 entries and is well-cited throughout the book. Unfortunately, the author sometimes relies on the bibliography too much. On page 392, the author brings up "the so-called graph isopomorphism disease" without defining it himself; he instead relies on his bibliography entries to give the user any definition or background on the "disease".

Unfortunately, the index received not nearly as much attention as the bibliography; neglecting whitespace, it's scarcely more than a single page long!

The book appears to be something more than a research paper, but is written much like a research apper would be. The book probably also serves well for a class that teaches this subject, and assumes LEDA and literate programming as prerequisites. But as a commercial developer who's interested in applying advanced graph and tree algorithms to the work I'm doing, I found the book has limited its value by relying on LEDA and applying literate programming.

Book Description

The subject of this book — intermolecular interactions — is as important in physics as in chemistry and molecular biology. Intermolecular interactions are responsible for the existence of liquids and solids in nature. They determine the physical and chemical properties of gases, liquids, and crystals, the stability of chemical complexes and biological compounds.

In the first two chapters of this book, the detailed qualitative description of different types of intermolecular forces at large, intermediate and short-range distances is presented. For the first time in the monographic literature, the temperature dependence of the dispersion forces is discussed, and it is shown that at finite temperatures the famous Casimir-Polder asymptotic formula is correct only at narrow distance range. The author has aimed to make the presentation understandable to a broad scope of readers without oversimplification. In Chapter 3, the methods of quantitative calculation of the intermolecular interactions are discussed and modern achievements are presented. This chapter should be helpful for scientists performing computer calculations of many-electron systems.

The last two chapters are devoted to the many-body effects and model potentials. More than 50 model potentials exploited for processing experimental data and computer simulation in different fields of physics, chemistry and molecular biology are represented. The widely used global optimisation methods: simulated annealing, diffusion equation method, basin-hopping algorithm, and genetic algorithm are described in detail.

Book Description

Combustion is an old technology, which at present provides about 90% of our worldwide energy support. Combustion research in the past used fluid mechanics with global heat release by chemical reactions described with thermodynamics, assuming infinitely fast reactions. This approach was useful for stationary combustion processes, but it is not sufficient for transient processes like ignition and quenching or for pollutant formation. Yet pollutant formation during combustion of fossil fuels is a central topic and will continue to be so in the future. This book provides a detailed and rigorous treatment of the coupling of chemical reactions and fluid flow. Also, combustion-specific topics of chemistry and fluid mechanics are considered and tools described for the simulation of combustion processes.

The actual fourth edition presents a completely restructured book: Mathematical Formulae and derivations as well as the space-consuming reaction mechanisms have been replaced from the text to appendix. A new chapter discusses the impact of combustion processes on the earth’s atmosphere, the chapter on auto-ignition is extended to combustion in Otto- and Diesel-engines, and the chapters on heterogeneous combustion and on soot formation appear heavily revised.

Customer Reviews:

Useful book.......2007-08-17

This book is not a complete guide but is a good self-learning help.
It can be also used as a quick reference.
A good starting point for combustion studies. Then other books are required if complete treatment is required.
Small but nice part of useful mathematics in appendix. Not a rigorous treatment but quick explanation of some topics related to CFD.

Combustion modeling review.......2000-04-08

This is a very good book. It format is very succictinct and as such spares no space for unecessary content. This give the narrative a somewhat terse style. It must be remembered that the science of combustion wrestles with some formidable concepts; such as turbulent flow, reduced reaction mechanisms for complex chemical reactions, fluid flow and heat transfer. This is not a book for those who are easily frightened by close typed differential equations. This book however, is an excellent introduction to the science of combustion, and contains a detailed and upto date biblography, pointing the interested reader in the right direction. It also contains one of the most complete tables of kinetic data for combustion reactions, I have seen in published literature. My one regret is that there is no companion volume of solved examples that could be used by an unassisted, but interested student. Read in conjunction with Smith/Missen, computation of chemical equilibrium, and Anderson's excellent introduction to Computational fluid dynamics, and the world of this facinating and most important field opens up.

Recent Advances in Coupled-Cluster Methods (Recent Advances in Computational Chemistry, Vol. 3)

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Recent Advances in Coupled-Cluster Methods (Recent Advances in Computational Chemistry, Vol. 3)

Manufacturer: World Scientific Publishing Company
ProductGroup: Book
Binding: Hardcover

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ASIN: 9810231121

Book Description

Today, coupled-cluster (CC) theory has emerged as the most accurate, widely applicable approach for the correlation problem in molecules. Furthermore, the correct scaling of the energy and wavefunction with size (i.e. extensivity) recommends it for studies of polymers and crystals as well as molecules. CC methods have also paid dividends for nuclei, and for certain strongly correlated systems of interest in field theory.

In order for CC methods to have achieved this distinction, it has been necessary to formulate new, theoretical approaches for the treatment of a variety of essential quantities. These include properties and, particularly, analytical first derivatives (gradients) that readily provide the forces on the atoms in a molecule to facilitate searching potential energy surfaces for structures and transition states; second derivatives (Hessians) which indicate the type of extremum point and provide vibrational frequencies and intensities; excited, ionized, and electron attached states including their properties; multi-configurational reference functions to add important non-dynamic correlation; and relativistic effects.

This book addresses very recent work in each of the above topics in ten chapters written by leading experts in molecular CC theory. This is NOT a collection of reviews, but is, instead, forefront research explained in an unusually clear exposition. Each chapter presents new results and formulations that offer another step toward providing the next generation of powerful CC solutions.

Book Description

Process Modelling and simulation have proved to be extremely successful engineering tools for the design and optimisation of physical, chemical and biochemical processes. The use of simulation has expanded rapidly over the last two decades because of the availability of large high-speed computers and indeed has become even more widespread with the rise of the desk-top PC resources now available to nearly every engineer and student.

In the chemical industry large, realistic non-linear problems are routinely solved with the aid of computer simulation. This has a number of benefits, including easy assessment of the economic desirability of a project, convenient investigation of the effects of changes to system variables, and finally the introduction of mathematical rigour into the design process and inherent assumptions that may not have been there before.

'Computational Methods for Process Simulation' develops the methods needed for the simulation of real processes to be found in the process industries. It also stresses the engineering fundamentals used in developing process models. Steady state and dynamic systems are considered, for both spatially lumped and spatially distributed problems. It develops analytical and numerical computational techniques for algebraic, ordinary and partial differential equations, and makes use of computer software routines that are widely available. Dedicated software examples are available via the internet.

Written for a compulsory course element in the US
Includes examples using software used in academia and industry
Software available via the Internet

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