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)

Average customer rating:

Outstanding introduction
A long expected book in molecular modeling is finally here
Beautifully written!
Never short of something exciting
Excellent book for both students and researchers

Molecular Modeling and Simulation
Tamar Schlick
Manufacturer: Springer-Verlag New York, Inc.
ProductGroup: Book
Binding: Hardcover

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ASIN: 038795404X

Book 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 by computational 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 computer science. 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 dynamics approaches. 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

Customer Reviews:

Outstanding introduction.......2004-05-13

... 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.......2004-02-17

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!.......2003-08-11

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.

Never short of something exciting.......2003-08-11

It contains many many exiting problems and stimulate to go through the world of art of biology and mathematics. This book can guide the way where to go when you lost in the world of biomathematics, specifically molecular modeling. It looks like a well-organized dictionary with analysis. So it is good for a beginner and also deep-thinker in computational biology field.

Excellent book for both students and researchers.......2003-08-08

This book covers state-of-arts technologies used in today's hot field: molecular modeling. The book is easy to understand and it is suitable for graduate students in both theoretic majors and experimental majors. The homeworks in the book are practical for students to learn basic molecular modeling computer skills very fast.

Book Description

This best-selling volume presents the principles and applications of physical chemistry as they are used to solve problems in biology and medicine. The First Law; the Second Law; free energy and chemical equilibria; free energy and physical Equilibria; molecular motion and transport properties; kinetics: rates of chemical reactions; enzyme kinetics; the theory and spectroscopy of molecular structures and interactions: molecular distributions and statistical thermodynamics; and macromolecular structure and X-ray diffraction. For anyone interested in physical chemistry as it relates to problems in biology and medicine.

Customer Reviews:

Complete Solutions Manual in the Collectible Section is worth its weight in GOLD!.......2007-02-12

Hi everyone, I just got my exam score emailed to me from Physical Chemistry (the one with some calculus involved). Guess what? I got a 96%. The class average was 45%. The professor told me my exam had the highest score ever in this class.

I found that all the test had were problems from the book. I remember procrastinating and not getting any studying done. So the night before the exam, I just memorized all the solutions, and I got a 96%.

The professor told me to get an A in the class, all I need to do is get above a D on the next 2 exams. Man, what a relief. My friends envy me, my professor worships me, and I owe it all to this solutions manual.

I was at first skeptical about its price, but it was worth so much more. Can you put a price on getting an A? Can you? Can you really? Its going to be alot more than $120, which was how much I paid for the well-needed solutions manual.

I just hope too many students don't get the manual, because then professors might figure out that there is a solutions manual (my professor has NO IDEA THIS BOOK HAS A SOLUTIONS MANUAL!).

So if you do end up getting the manual, just use it for yourself, don't even show your friends or bring it to class. Just use it on your own, memorize the solutions, get your A+ in the class, tell all your friends and your professor that you just studied VERY HARD, and leave it at that.

The less the number of people that know about this solutions manual, the better. Also, since this was my first time using amazon.com, make sure that when you add the item to your card, the description should say "SOLUTIONS MANUAL." I bought it from the collectible section, and in the description it said that it was the "complete solutions manual."

Good luck in mastering physical chemistry;I won't need luck, I got the solutions manual!

Get the SOLUTIONS MANUAL; Best decision I ever made in my ENTIRE LIFE. ONLY one in my class who got an A, let alone an A+.......2006-10-01

Hello mates,

I don't write any reviews, but when I got my first physical chemistry test back to day, I just had to write this out. THIS BOOK WAS IN THE COLLECTIBLE SECTION OF THE NEW AND USED SECTION. All my test had were questions from the book, and some that were very much like the book (only changed numbers). I procrastinated to study as usual, and all I did was study the solutions manual, and I was the ONLY STUDENT TO GET AN A+. THE ONLY ONE IN THE CLASS. My professor asked me to become a tutor, and now I'm getting paid.

All in all, physical chemistry is tough, BUT you WILL GET AN A with the solutions manual! You have my word, and my experience to prove it.

Excellent Solutions Manual; Helped me get an A+ without much work!.......2006-09-29

When I received it, OH MY GOD, it had DETAILED ANSWERS to every single problem in the book. Whats more, my physical chemistry course had questions from the book on its test, and all I did was memorize the solutions and got an A+. I can't believe it!

I even corrected my professor on a few problems; my professor didn't even know there was a solutions manual and I wasn't about to tell him there was.

All in all, I just wanted to post my awesome experience. It was a great help. Just like in Physics, Chemistry, or biology, a solutions manual can only augment your skills. Plus it wasn't too long, about 100 pages.

Also, the other reviewer who said the solutions manual was bad must've bought another edition (older one), because the solutions manual I received had ALL THE SOLUTIONS to ALL THE PROBLEMS in COMPLETELY WORKED OUT form.

someone really did only for the money or ...........2005-10-15

simply this book is terrible.

despite the impression the publisher wanna impose on the readers by citing the authors' notable teaching positions, it immediately loses whole credibility it tries to establish as a decent book by failing too soon in every respect, begining from the chapter 2.

i have read two other p.chem books and personally do not like the babish differential appoaches all of them give out invariably and rather forcing the concept that differential operators are "infinitesimal quantities." I understand that authors chose this crude and uber-ancient interpretation(along with other mathematical nonsenses) to reach the widest audience possible but this sort attempt makes the book fraught with confusing junks. And this particular book does not fail to follow this safe yet confusing approach. However, unlike other p.chem texts(at least for the atkin's and levine's) it abuses the mathematical notations and forces equations by ignoring constraints to come up with formulas. For example, to derive the partials of the extensive functions(chapter 4) it just intergrate all the different partials(dual base coeffients and its corresponding dual base) and somehow comes up with definite integrals. Anyone who took decent calculus class would know that the inverse map of the differential map is not that simple unless the variables are not related to each other. Other texts at least offer the constraints, although not explicitly(this subsequently makes the unwary readers oblivious about the specific conditions in which the pertaining equation is applicable).

anyhoo, the book is way too superflous with mathematical nonsenses and tries really hard to get rid of diffcult concepts by presenting concepts as "definitions." More frusrating than this is the fact that it completely lacks the proper motivation building-up before presenting particular concepts or formulas. Perhaps the authors of this book are truly convinced that all the future-biochemist/MD wanna-bes are faithful believers of the ubiquitous yet unspoken notion that all of our current scientific knowledges are nothing more than mere remnants of forcefully fed informations on a few chosen human beings many years ago despite their vehement refusals.

Just buy another p-chem book and use a good biochem text(such as voet's) instead of using this book. Making connection between the physical chemistry and biological science is not that difficult. If you can't you always got internet.

Terrible Book.......2005-09-23

This is an absolutely horrible textbook, derivations and applications of physical chemistry equations are poorly explained. Very few examples of how to use the equations provided. This text was required for my second year Phys Chem course, and did nothing but confuse me!

Conformational Analysis of Molecules in Excited States

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Conformational Analysis of Molecules in Excited States
Jacek Waluk
Manufacturer: John Wiley & Sons
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471297070

Book Description

A unique look at some of the hottest topics in photophysics and photochemistry today

The study of molecules in excited states has exploded over the past decade, providing new insights into conformational changes in organic molecules and opening up research opportunities for scientists and professionals in chemistry, physics, biology, medicine, and materials engineering.

Using conformational analysis as a unifying concept, this important new work provides readers with a cohesive and cutting-edge overview of this fascinating and challenging field. From conformational changes accompanying photoinduced electron transfer to elementary photophysical and photochemical processes in living systems, the most representative and challenging topics are carefully gleaned from the vast literature, highlighting major conceptual problems along with the relevant experimental techniques. Authoritative, detailed contributions from both experimentalists and theoreticians include coverage of:
* Conformational changes in intramolecular excited state electron transfer
* Conformational aspects of excited state proton transfer
* The novel topic of solute-solvent friction in chemical reactions
* Mechanisms and structural aspects of exciplex formations
* Conformational aspects of organic photochemistry
* Calculations of excited state conformational properties

Molecular Fluorescence: Principles and Applications

Average customer rating:

great for beginners, but too few references

Molecular Fluorescence: Principles and Applications
Bernard Valeur
Manufacturer: John Wiley & Sons
ProductGroup: Book
Binding: Hardcover

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ASIN: 352729919X

Book Description

Today, fluorescence spectroscopy is an important tool of investigation in many areas. In analytical sciences, its advantage is extremely high sensitivity and selectivity - even single molecules can be detected - and it achieves a high spatial resolution and time resolution in combination with microscopic techniques or laser techniques, respectively. In material sciences, this is used to study structure and dynamics of surfaces. Particularly in the areas of biochemistry and molecular genetics, fluorescence spectroscopy has become a dominating technique. Together with the latest imaging techniques, fluorescence spectroscopy allows a real-time observation of the dynamics of intact biological systems with an unprecedented resolution.
This book offers a comprehensive introduction to and survey of fluorescence spectroscopy. It is written for newcomers and active researchers alike who are learning to apply fluorescence methods in the areas of chemistry, physical chemistry, polymers, materials, colloids, biochemistry, biology, medical and pharmaceutical research.

Customer Reviews:

great for beginners, but too few references.......2003-12-07

This is a great introductory book. Beautifully edited, very well written, with a lot of information to start digging each subject; I just missed a few more references in each chapter, and also more references to journals and not just other books, and then I would have been a 5 star.

Spatio-Temporal Pattern Formation: With Examples from Physics, Chemistry, and Materials Science (Partially Ordered Systems)

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Spatio-Temporal Pattern Formation: With Examples from Physics, Chemistry, and Materials Science (Partially Ordered Systems)
Daniel Walgraef
Manufacturer: Springer
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Binding: Hardcover

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Book Description

This book provides an interdisciplinary presentation of the current knowledge of pattern formation in complex system, with sufficiently many details, tools, and concrete examples to be useful for the graduate student or scientist entering this area of research.

Progress In Thermochemical Biomass Conversion

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Progress In Thermochemical Biomass Conversion
A Bridgwater
Manufacturer: Blackwell Publishing
ProductGroup: Book
Binding: Hardcover

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ASIN: 0632055332

Book Description

This book is for chemical engineers, fuel technologists, agricultural engineers and chemists in the world-wide energy industry and in academic, research and government institutions. It provides a thorough review of, and entry to, the primary and review literature surrounding the subject. The authors are internationally recognised experts in their field and combine to provide both commercial relevance and academic rigour. Contributions are based on papers delivered to the Fifth International Conference sponsored by the IEA Bioenergy Agreement.

Computational Biology Of Cancer: Lecture Notes And Mathematical Modeling

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Computational Biology Of Cancer: Lecture Notes And Mathematical Modeling
Dominik Wodarz , and Natalia L. Komarova
Manufacturer: World Scientific Publishing Company
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Binding: Hardcover

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ASIN: 9812560270

The Elements of Physical Chemistry: With Applications in Biology

Average customer rating:

the book is a mess
Informative and provolking

The Elements of Physical Chemistry: With Applications in Biology
Peter Atkins
Manufacturer: W. H. Freeman
ProductGroup: Book
Binding: Hardcover

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ASIN: 0716735385

Customer Reviews:

the book is a mess.......2003-10-19

I feel compelled to add my two cents because this textbook has been such a nightmare to use. It completely lacks any rational organizational structure. It strikes me as the culmination of the work of a competent chemist but poor author working with an even more atrocious editor. Working the problems requires hunting down tables buried in other chapters and is often made more difficult by numerous errors in the solutions manual. It is so bad I am counting the days until I can get rid of it.

Informative and provolking.......2001-07-13

Atkin's analysis of the integration of physical chemistry and biology I believe made a much better model for future biophysics. The text is an informative resource for one, and also an excellent educational tool. Also, its implications are almost frightening in their scope and degree. This was an excellent book, indeed. It is still an excellent text, and probably will be a worthwhile read for many years to come.

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