Product Description
Molecular modeling is becoming an increasingly important part of chemical research and education as computers become faster and programs become easier to use. The results, however, have not become easier to understand. Addressing the need for a "workshop-oriented" book, Molecular Modeling Basics provides the fundamental theory needed to understand not only what molecular modeling programs do, but also the gist of research papers that describe molecular modeling results.

Written in a succinct manner using informal language, the book presents concise coverage of key concepts suitable for novices to the field. It begins by examining the potential energy surface (PES), which provides the connection between experimental data and molecular modeling. It explores ways to calculate energy by molecular and quantum mechanics. It describes molecular properties and the condensed phase, and shows how to extract and interpret information from a program output. The author uses hands-on exercises to illustrate concepts and he supplements the text with a blog containing animated tutorials and interactive figures.

Drawn from the author’s own lecture notes from a class he taught for many years at the University of Iowa, this volume introduces topics in such a way that beginners can clearly comprehend molecular modeling results. A perfect supplement to a molecular modeling textbook, the book offers students the "hands-on" practice they need to grasp sophisticated concepts. ... Read more

Product Description
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 ... Read more

Product Description
Ideal for beginners, this book explains the basics of modeling in a competent yet easily understandable way. Following complete sections on the modeling of small molecules, protein modeling and chemogenomics, completely worked-out examples show the way to the reader's first modeling experiment.

This new, third edition features a new chapter on chemogenomics, reflecting the trend towards 'chemical biology', as well as the protein modeling example being completely rewritten for a better 'feel' of modeling complex biomolecules.

The authors are experienced university teachers who regularly hold courses on molecular modeling, making this a tried-and-tested text for teachers. It is equally valuable for experts, since it is the only book to evaluate the strengths and limitations of the molecular modeling techniques and software currently available. ... Read more

Customer Reviews (2)

Useful textbook
Well, I had both 2nd and 3rd edition of this book and I think that this is a good introduction to molecular modeling. If you are searching for a cook book, leave this aside. Also, if you already have nice experience in the field, this would be a dull reading material for you. But, if you are a hard core bench chemist wondering how they do it with those computers and what the heck can they actually do or you are a novice wanting to get an insight to molecular modeling, this is a nice book for you. Lots of references (that were fresh when the book was issued), easy reading, nice style makes this book very useful as some basic molecular modeling course material.
Not so good things: it would be nice if there are more case studies, and most useful would be those using tools and things available to larger academic (read: with lower budget) auditorium, like students.
Nevertheless, I'll go for a 4 stars, this is a good book.

Accelrys advertisement
This book describes what is essentially docking calculations in the context of the Accerlys software.The text is very qualitative and does not provide enough instruction to do any "molecular modeling".It seems to be more guidlines for various software packages sold by Accerlys. ... Read more

Product Description

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.

Product Description
This book evolved from an interdisciplinary graduate course entitled Molecular Modeling developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while introducing readers to the wide range of biomolecular problems being solved bycomputational techniques and to those computational tools. The book is intended for beginning graduate students in medical schools and scientific fields such as biology, chemistry, physics, mathematics, and computerscience. Other scientists who wish to enter, or become familiar, with the field of biomolecular modeling and simulation may also benefit from the broad coverage of problems and approaches.

The book surveys three broad areas: biomolecular structure and modeling: current problems and state of computations; molecular mechanics: force field origin, composition, and evaluation techniques; and simulation methods: geometry optimization, Monte Carlo, and molecular dynamicsapproaches. Appendices featuring homework assignments, reading lists, and other information useful for teaching molecular modeling complement the material in the main text. Extensive use of world wide web resources is encouraged, and additional course and text information may be found on a supplementary website.

Some praise for Tamar Schlick's "Molecular Modeling and Simulation: An Interdisciplinary Guide":||"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling."|-Harold A. Scheraga, Cornell University||"A uniquely valuable introduction to the modeling of biomolecular structure and dynamics. A rigorous and up-to-date treatment of the foundations, enlivened by engaging anecdotes and historical notes."|-J. Andrew McCammon, Howard Hughes Medical Institute, University of California at San Diego||"I am often asked by physicists, mathematicians and engineers to recommend a book that would be useful to get them started in computational molecular biology. I am also often approached by my colleagues in computational biology to recommend a solid textbook for a graduate course in the area. Tamar Schlick has written the book that I will be recommending to both groups. Tamar has done an amazing job in writing a book that is both suitably accessible for beginners, and suitably rigorous for experts."|-J.J. Collins, Boston University

FROM THE REVIEWS:

BIOTECH INTERNATIONAL [BTI]:" . . . The text emphasises that the field is changing very rapidly and that it is full of exciting discoveries. Many of these findings have lead to medical and technological breakthroughs. This book stimulates this excitement, while still providing students many computational details . . . It should appeal to beginning graduate students in medical schools, and in many scientific departments such as biology, chemistry, physics, mathematics, and computer science. ... Read more

Customer Reviews (12)

The protein folding problem best source!
This book is extremely informative, well-writen and clear on explaining the 3D structural biology of life, Monte carlo and mol dynamics methods on how to simulate its conformational space and limitations of this area of research.An exciting new book in a very exciting field.

Lots of stuff to read, less to understand
The book is quite long and seems informative, however I did not get what I wanted. It should be a modeling and simulation book, but it has so little info about forcefields in molecular dynamics for example...

I would suggest buying the books by Andrew Leach or Frenkel and Smit.

Outstanding introduction
... not only to molecular modeling, but to some of the subtleties of DNA and protein behavior and geometry, too.

This book's focus is generally on interactions with large molecules, DNA and proteins, although it does discuss small molecules (drugs, a few dozen to a few hundred atoms) too. That means that it skips most of the quantum mechanical modeling of more advanced computational chemistry texts.

Nothing is lost, because Schlick covers her chosen topic (molecular modeling and dynamics) in such detail. She starts with a very clear discussion of the structure of large biomolecules, with emphasis on the features that need quantitative description for modeling. That covers protein structure at ever level. It also covers DNA/RNA structure in the best detail I've ever seen. The double-helix is the just the starting point. There are alternative helix forms, non-standard binding between nucleotides, and asymmetries caused by nucleotide composition. The next chapters describe the geometric model and, briefly, the forces acting between atoms.

The second half of the book gets down to the nuts and bolts of modeling. This includes numerical techniques, minimization, sampling and Monte Carlo techniques, and the start of dynamics. Schlick attacks some of the nasty points of the calculations, such as modeling of forces that act on very different time scales. As with the simpler material, the development is clear, descriptive, and free of pointless theorems. The meticulous reader should come away able to implement most or all of the techniques described. The level of presentation is consistent and approachable. I think freshman physics should be enough preparation for most students to get most of the value out of the discussion.

The book is written with clarity as a top priority. The glossary is in the front, making sure that the reader knows it's a first-class part of the text. After that, every chapter starts with a list of the mathematical symbols and variables used and a one-line description of each. These are small things, but they increase the book's readability immensely. The illustrations are generally informative enough. On the whole, though, they don't seem quite up to the level of the textual and mathematical presentations.

I needed a crash course in the mathematical techniques used for describing molecular structure and behavior. I should have read this book first - its clarity and thoroughness would have saved me a lot of time. After this one, I can now go back and reread the more complex texts with more hops of understanding. Do yourself a favor and read this one first.

A long expected book in molecular modeling is finally here
I highly recommend Professor T. Schlick's book. It is beautifully written with many examples and great illustrations. The book is truly interdisciplinary; it covers, in good depth, both the biological and mathematical aspects of computational structural biology. Most chapters start with an amenable introduction and finish with "hands-on" recommendations and future challenges. I was particularly pleased with the level of detail in each chapter (in particular those that show the reader the advantages and pitfalls of the different methods presented). My colleague Mariel Vazquez and I used this book in the design and preparation of our "Special topics in Mathematics" course at the UC Berkeley Mathematics Department during the Spring of 2003.

This upper-level undergraduate/lower-level graduate course was centered on mathematical and computational models of the three dimensional structure of DNA, and DNA topology. We found Professor T. Schlick's book very useful in our class preparation. In particular we covered chapter 5 (DNA structure) completely, sections 3 and 4 from chapter 7 (basic principles and formulation of atomic interactions in molecular mechanics), and several sections or subsections from chapters 8 and 9 (force terms used in molecular dynamics simulations). We also covered most of the material in chapter 10 (Multivariate Minimization), and gave a brief introduction to chapter 11 (Monte-Carlo techniques) and chapter 12 (Molecular Dynamics algorithms).

Chapter 5 starts with a very amenable and brief introduction that relates DNA with other biological processes and describes some of the challenges in studying DNA structure. It continues describing the basic building blocks of DNA. The author wisely spends some time defining the nomenclature for each of the atoms, angles and bonds that form these basic blocks. The following sections teach the reader what parameters are relevant for describing a DNA double helix and how they characterize the A, B and Z- forms of DNA. Illustrations in this chapter are particularly helpful.

Although our course's approach to DNA supercoiling was different that the one in the book I found particularly useful some illustrations in chapter 6 and movies (to be found in her webpage) that Prof. Schlick's group has developed over the years. In brief, chapter 6 is a study of more complex structures and behavior of DNA (such as structural role of the DNA sequence, DNA-protein interactions, and higher order organization of DNA -i.e. DNA supercoiling and histone-DNA interactions). This chapter can be a good source for short research projects (e.g. final projects).

Chapters 7, 8 and 9 describe the basic concepts in molecular mechanics. From sections 7.3 and 7.4 I found of interest how the author addresses the problem of the system size (i.e. number of interacting molecules) and some of the details that the author gives for modeling the geometry of atomic interactions. At the end of the chapter (section 7.4.3) interested readers can find some of the limitations of current approaches. Chapters 8 and 9 describe in depth the force fields and how to implement them.Chapter 9 also illustrates with clarity how to implement periodic boundary conditions and the advantages of using different lattice models.

Chapter 10 describes a number of familiar methods for energy minimization (i.e. steepest descent, conjugate gradient, etc....). We used sections 10.1 to 10.4 and section 10.5.2 (conjugate gradient). I found the Hessian patterns shown in figures 10.4 and 10.5 and the minimization trajectories shown in 10.10 very pedagogical. As in previous chapters the author finishes with practical recommendations and future challenges.

We left chapter 11 (Monte Carlo methods) for last in the course and discussed chapter 12 (molecular dynamics) first. As in previous chapters the author gives a very nice introduction (section 12.1 and 12.2) and covers the basics on simulation protocols in sections 12.3 and 12.4. Section 12.4 describes the basic integration algorithms such as leap-frog, verlet, etc... Figure 12.3 was revealing for the students as it compares the time scales in biological systems.

Chapter 11 (Monte-Carlo methods) provides a very comprehensive introduction to Monte-Carlo methods. We found particularly useful some of the subsections of random number generation and the treatment of Importance sampling and Markov chains in section 11.5.

As mentioned earlier we were particularly delighted with the amount of details given in each topic. For example chapters 7 and 8 provide all the formalism needed for the problems of molecular mechanics.In section 8.4 (bond angle potential) the author highlights the differences (both formally and by figures-see figure 8.4) between different formulations of the problem (see also figure 8.6). In Chapter 10 the author describes minimization algorithms in detail and shows some of the patterns that one observes in the Hessian associated to minimization functions of biological structures (see figs. 10.4, 10.5 and 10.11). She also makes very detailed comparisons between the different minimization methods (see figs 10. 2, 10.10). In chapter 12 she compares the different methods and initial conditions for the algorithms discussed (figs 12.3, 12.4, 12.6).

Overall we found that Prof. T. Schlick's book is very adequate for a broad spectrum of levels and very accessible to both graduate and undergraduate students interested in mathematical modeling and computational biology. It is also very well organized facilitating the option of selecting parts of the material for the classroom or for use in one's research.

Beautifully written!
As a person with no expertise in molecular modeling who wanted to learn about this field, this book is right on!I find the author's lively text to be as well-written and clear as any science textbook I have ever read.I especially enjoyed the first two chapters for their historical perspective and their practical illustrations of applications of genetics in the world today.These chapters can be understood by non-scientists, whereas the rest of the book is clearly designed for graduate students in any one of the science disciplines.

The interesting information sprinkled throughout the book, including the boxes and figures, help keep the reader stimulated and yearning for greater knowledge of this exciting field.The color graphics also complement the book nicely.Although the subject covered in the book is extremely broad, the author managed to convey the perspectives of multiple scientific disciplines (e.g., biology, chemistry, computer science, math) very well.The combination of breadth and depth in a readable style is remarkable.

Overall, I highly recommend this book to readers interested in the area. ... Read more

Product Description
* Manufactured by Darling Model Kits, this custom kit was designed by T.W.Graham Solomons.
* The kit consists of Darling's basic Molecular Vision kit with a few additional pieces, so that p orbitals could be shown in molecules like acetylene.
* This customized kit also has pieces that allow linear geometry for the sigma bonds of alkynes while also having orthogonal connections at each atom for the associated p orbitals.
* By attaching balls of the right colors it is possible to show the lobes of the p orbitals that make up the pi bonds in an alkyne.
* Ball colors can be matched symmetrically to show in-phase orbital overlap, or antisymmetrically to show an antibonding state.
* Use of colored balls with the appropriate framework geometry is a very nice feature of the Darling model set.
* Pieces from Darling's inorganic model set and are used for octahedral geometry. ... Read more

Customer Reviews (16)

Molecular Model Kit
This product comes with a card board box that you have to build your own to put all your pieces in. Some directions are on the outside of this box and it is hard to read, and the instruction book isn't straight forward if you just want to skim through it. I had trouble finding what I wanted in it. The pieces are fine but the sp3 pieces started to bend a little after rotating between chairs of a cyclohexane.

Not USEFUL; Horrible; WORST EVER; DON"T BUY
This molecular model kit sucks!! You cant even rotate stuff around freely. It's so hard to assemble a carbon with 4 attachments (SOMETHING THAT IS VERY BASIC). It is a piece of crap. If you go to any serious top 20 university and you try to use this molecular model kit, you will fail. DO NOT BUY. PAY A LITTLE EXTRA TO BUY A BETTER ONE OR TRY TO BORROW ONE FROM YOUR FRIENDS!! THIS KIT IS THE WORST EVER!!!!!!!!!!!!!

Better than anything else out there
While hunting for a modeling kit for my organic class, I initially skipped over this one based on all of the negative reviews. I initially went with a similarly priced kit with many more pieces and much better reviews. However, upon receiving that set, I found that all of the pieces were tiny, and frustrating and painful to put together. I looked for others, trying to avoid this kit, but all of the college-student affordable ones were similar, with lots if minuscule pieces.

In contrast, after getting this one, I found that this kit has solid feeling (for plastic) pieces that are large enough to easily assemble molecules with. Sure, it might have fewer pieces, but is preferable than "miniature" kits that are simply hard to use. If switching from the plastic box to a cardboard folding box saves them money, so be it! I have not found a modeling kit that compares in this price range.

Not exactly as pictured, but good enough
I purchased this kit through amazon because it beat my bookstore price at the college by nearly ten bucks. The picture i saw depicted it in the plastic case as it is sold here, however it shipped with a piece of cardboard that folds very intricately into a cheap, tiny little box.has all pieces and manuals intact, so it will work good enough for me.

Horrible
This molecular model kits is plain horrible. First of all, it comes in a plastic bag, not case like many of its competitors. Furthermore, the molecules created by this kit do not stay together. It is almost unusable. ... Read more

Product Description
The dynamic development of various processes is a central problem of biology and indeed of all the sciences. The mathematics describing that development is, in general, complicated, because the models that are realistic are usually nonlinear. Consequently many biologists may not notice a possible application of theory. They may be unable to decide whether a particular model captures the essence of a system, or to appreciate that analysis of a model can reveal important aspects of biological problems and may even describe in detail how a system works. The aim of this textbook is to remedy the situation by adopting a general approach to model analysis and applying it several times to problems (drawn primarily from molecular and cellular biology) of gradually increasing biological and mathematical complexity. Although material of considerable sophistication is included, little mathematical background is required - only some exposure to elementary calculus; appendixes supply the necessary mathematics and the author concentrates on concepts rather than techniques. He also emphasizes the role of computers in giving a full picture of model behavior and complementing more qualitative analysis. Some problems suitable for computer analysis are also included. This is a class-tested textbook suitable for a one-semester course for advanced undergraduate and beginning graduate students in biology or applied mathematics. It can also be used as a source book for teachers and a reference for specialists. ... Read more

Product Description
In the past two decades, new modeling efforts have gradually incorporated more molecular and structural detail in response to environmental and technical interests. Molecular Modeling in Heavy Hydrocarbon Conversions introduces a systematic molecule-based modeling approach with a system of chemical engineering software tools that can automate the entire model building, solution, and optimization process.

Part I shows how chemical engineering principles provide a rigorous framework for the building, solution, and optimization of detailed kinetic models for delivery to process chemists and engineers. Part II presents illustrative examples that apply this approach to the development of kinetic models for complex process chemistries, such as heavy naphtha reforming and gas oil hydroprocessing.

Molecular Modeling in Heavy Hydrocarbon Conversions develops the key tools and best possible approaches that process chemists and engineers can use to focus on the process chemistry and reaction kinetics for performing work that is repetitive or prone to human-error accurately and quickly. ... Read more

Customer Reviews (1)

Very Interesting
This book show a very interesting methodology for modeling complex feedstok, from tecnical ponit of view could be very usefull to solve some engeneering problems ... Read more

Product Description
This text provides an introduction for chemists with a limited mathematical background, yet who need a working understanding of quantum chemistry as applied to problems in organic chemistry. It covers molecular modelling software, and offers a guide to the scope of each program. ... Read more

Product Description
This self-contained work is an up-to-date treatment of the basic theory of molecular gas dynamics and its various applications. Recent progress in the field has greatly enhanced the original theory and stimulated interesting and critical gas dynamic phenomena and problems. This book, unique in the literature, presents working knowledge, theory, techniques, and typical phenomena in rarefied gases for theoretical development and applications.Basic theory is developed in a systematic way and presented in a form easily applied to practical use. After presenting basic theory and various simple flows, such as unidirectional or quasi-unidirectional flows and flows around a sphere, the author discusses additional topics, including flows induced by temperature fields, which are typical in rarefied gases; flows with evaporation and condensation; and bifurcation of flows in rarefied gases. The appendix contains many useful fundamental formulae, as well as an explanation of the theoretical background for the direct simulation Monte Carlo (DSMC) method, easily accessible to nonmathematicians and not found elsewhere in the literature.Existence of the ghost effect has made molecular gas dynamics indispensable to the study of a gas in the continuum limit, traditionally treated by classical fluid dynamics. In this book, the ghost and non-Navier–Stokes effects are demonstrated for typical examples—such as Bénard and Taylor–Couette problems—in the context of a new framework. An infinitesimal curvature effect is also discussed, with a long-standing problem of the bifurcation of the plane Couette flow worked out as an example.Molecular Gas Dynamics is useful for those working in different communities where kinetic theory or fluid dynamics is important: graduate students, researchers, and practitioners in theoretical physics, applied mathematics, and various branches of engineering. The work may be used as a self-study reference or as a textbook in graduate-level courses on fluid dynamics, gas dynamics, kinetic theory, molecular or rarefied gas dynamics, microflows, and applied mathematics. ... Read more

Product Description
Presents critical accounts of heterocyclic compounds. Topics include QSAR and molecular modeling studies of factor Xa and thrombin inhibitors; structural information and drug-enzyme interaction of the non-nucleoside reverse transcriptase inhibitors based on computational chemistry approaches; and more. For researchers. ... Read more

Product Description

The gap between introductory level textbooks and highly specialized monographs is filled by this modern textbook. It provides in one comprehensive volume the in-depth theoretical background for molecular modeling and detailed descriptions of the applications in chemistry and related fields like drug design, molecular sciences, biomedical, polymer and materials engineering. Special chapters on basic mathematics and the use of respective software tools are included. Numerous numerical examples, exercises and explanatory illustrations as well as a web site with application tools (http://www.amrita.edu/cen/ccmm) support the students and lecturers.

Customer Reviews (4)

Non traditional student
Caution:The main picture advertising this product shows a green plastic box with a very large assortment of pieces.The product shipped is a small cardboard box with few pieces.If you go back to the other pictures, which you have to click on to enlarge, you can see the cardboard box.I find it disingenuous that the first, enlarged picture is the prominent one.Do you think this is an accident?I don't.I hate deception in advertisingMolecular Visions Organic Modeling Kit.
Ted

No green plastic box.
I like the kit itself since it is the one I used for my organic chemistry class, but the original I had came with a green plastic box.This kit arrived with a disappointing cardboard box.I have no idea how it will hold up.However, it is aesthetically less appealing, AND it is NOT what is shown in the picture.

disappointed
I'm actually quite disappointed in this kit. Even though it was only $12, I think I would have been happier spending the $40 for the Prentice Hall kit. The ease of putting the molecules together is ok but not as easy as the Prentice kit, in which you could better visualize where the bonds go and the according shape (whether it's tetrahedral or planar or linear). This kit requires more work from the student than is necessary. When you're studying you just want to be able to put the molecule together in a quick manner so you can get to the point of what you're doing, whether trying to visualize flips and rotations, but it's harder to do that with this one kit.

If you're on a budget, this kit isn't bad but I dread having to make a molecule because it's a fairly cheap kit and I say with some conservation.

Molecular Kit VERY helpful for Organic Chemistry Students
This kit goes perfectly with any organic chemitry class, in that it helps enormously to visualize practically any molecule, thereby alleviating the most common pain of organic chamistry students. Also great for children curious about chemistry. ... Read more

Product Description
In recent years chemical engineers have become increasingly involved in the design and synthesis of new materials and products as well as the development of biological processes and biomaterials. Such applications often demand that product properties be controlled with precision. Molecular modeling, simulating chemical and molecular structures or processes by computer, aids scientists in this endeavor. Volume 28 of Advances in Chemical Engineering presents discussions of theoretical and computational methods as well as their applications to specific technologies. ... Read more

Product Description

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

Product Description
Increasingly useful in materials research and development, molecular modeling is a method that combines computational chemistry techniques with graphics visualization for simulating and predicting the structure, chemical processes, and properties of materials.

Molecular Modeling Techniques in Materials Science explores the impact of using molecular modeling for various simulations in industrial settings. It provides an overview of commonly used methods in atomistic simulation of a broad range of materials, including oxides, superconductors, semiconductors, zeolites, glass, and nanomaterials. The book presents information on how to handle different materials and how to choose an appropriate modeling method or combination of techniques to better predict material behavior and pinpoint effective solutions. Discussing the advantages and disadvantages of various approaches, the authors develop a framework for identifying objectives, defining design parameters, measuring accuracy/accounting for error, validating and assessing various data collected, supporting software needs, and other requirements for planning a modeling project. The book integrates the remarkable developments in computation, such as advanced graphics and faster, cheaper workstations and PCs with new advances in theoretical techniques and numerical algorithms.

Molecular Modeling Techniques in Materials Science presents the background and tools for chemists and physicists to perform in-silico experiments to understand relationships between the properties of materials and the underlying atomic structure.  These insights result in more accurate data for designing application-specific materials that withstand real process conditions, including hot temperatures and high pressures. ... Read more

Product Description
The advent of ever more sophisticated molecular manipulation techniques has made it clear that cellular systems are far more complex and dynamic than previously thought. At the same time, experimental techniques are providing an almost overwhelming amount of new data. It is increasingly apparent that linking molecular and cellular structure to function will require the use of new computational tools.This book provides specific examples, across a wide range of molecular and cellular systems, of how modeling techniques can be used to explore functionally relevant molecular and cellular relationships. The modeling techniques covered are applicable to cell, developmental, structural, and mathematical biology; genetics; and computational neuroscience. The book, intended as a primer for both theoretical and experimental biologists, is organized in two parts: models of gene activity and models of interactions among gene products. Modeling examples are provided at several scales for each subject. Each chapter includes an overview of the biological system in question and extensive references to important work in the area. ... Read more

Customer Reviews (3)

Informative, but not information I can use
Regulatory networks are central to every aspect of computational biology. Determining what they are, and what genes, proteins, and post-translational modifications interact is a major and exciting field of study.

I just didn't come away from this book with that excitement. I was hoping for more about the large-scale regulation networks, but these papers go down to the quantum mechanics of interactions between pairs of molecules. I appreciate that the exact interactions matter, and that computation is probably the only way to examine some kinds of interactions (e.g. the ones in lethal mutations). It's just not what I think of as a "network."

I was also hoping for some more specifics about the computation techniques. There were some interesting insights here. For example, I never thought about the similarities between steady state chemical equilibrium and steady state Markov model behavior before, but the formalisms have striking similarities. I was also interested in some of the information-based measures for determining how well a model represents a system. I learned that the statistical assumptions behind normal chemical "equilibrium" break down at the scale of bacteria - instead, presence or absence of individual molecules matters more. Still, those were isolated kinds of facts and never came together into a whole for me.

The range of views was worthwhile. On the whole, though, the models all seemed very low-level to me, probably not well suited to handling more than a few dozen interactions, and the computation specifics were not always explicit. I'm still looking for a book with more information that I can apply directly.

Excellent survey of the field
An excellent survey for anyone contemplating doing research in this area.The authors make a special effort to identify the open research problems, what has been done to date and what there is very little of.This book will bridge the gap for anyone with a background in Molecular Biology that wants to build computer models for cellular and genetic activities.It is especially focused on gene regulation, but also covers other modeling areas such as diffusion.In reading this book, you will appreciatge both the good start this field is off to, but also the long way to go before a complete cell can be modeled.A great area to do pioneering work.

it's about time!!!
For many years, biologists have been accumulating descriptions of biological "parts" with an almost complete lack of a framework for understanding how those parts might really work together.This book represents the first and so far only example I have seen of an effort to describe modeling techniques that are right now being developed to construct such a framework.There are other books on "computational biology", but most of them are focused only on measuring and comparing different strands of molecules-- this book describeshow computational techniques are starting to be applied to actually trying to understand how those molecules work together to generate life. On the outside jacket of the book, Bruce Alberts, President of the National Academy of Science, AND the guy whose book on molecular biology I had to buy for a lot of money when I was in college, describes the authors of this book as being "Brave".I would say it is an introduction to a "Brave New World".This has to be where biology is going -- Each of the chapters are written by different people, and as such there is some variation in readability.I also wish that the color illustrations were part of the chapter they refer to instead of being grouped in the middle.But most of the chapters start with enough of an overview to be understandable to anyone with a decent background in biology.And WOW -- biology is going to get much more exciting!! Oh one other thing -- the art on the inside of the jacket is wonderful - especially in contrast to the black cover with its standard diagram of metabolism -- I wonder if there is a message there:-) . ... Read more

Customer Reviews (1)

Fundamental ofComputational Chemistry
Is the best book for start to learn molecularmodeling. Is a excelent for undergraduate student ... Read more