Molecular Modeling and Simulation [Hardcover]

Tamar Schlick (Author)

Book Description

ISBN-10: 038795404X | ISBN-13: 978-0387954042 | Publication Date: August 19, 2002 | Edition: 1

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

Editorial Reviews

Review

From the reviews:

HAROLD A. SCHERAGA, CORNELL UNIVERSITY

"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling."

 

J. ANDREW McCAMMON, HOWARD HUGHES MEDICAL INSTITUTE, UNIVERSITY OF CALIFORNIA AT SAN DIEGO

"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.J. COLLINS, BOSTON UNIVERSITY

"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."

 

BIOINFORMATICS

"It is a fantastic graduate textbook to get into structural biology. The 14 chapters offer keys to understand the broader context of this field and the impact it can have on our everyday life for example through medical applications…The main achievement of the book is that even the most sophisticated problems are part of a gradual approach…certainly efficient…The book will obviously be of great interest to students and teachers but it should also be very valuable for research scientists, especially newcomers to the field of molecular modeling, as a reference book and a point of entry in the more specialized literature."

 

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.

 

MATHEMATICAL REVIEWS

Review by Henry van den Bedem, University of Alabama-Birmingham

"The book is unique in that it combines introductory molecular biology with advanced topics in modern simulation algorithms in no more than 600 pages. … For those seeking more detail, the author provides 1000+ references, and additionally includes reading lists complementing the main text. This is an excellent introductory text that is a pleasure to read."

 

ZENTRALBLATT MATH

Review by Ivan Krivy, University of Ostrava, Czech Republic

"This book provides an excellent introduction to the modeling of biomolecular structures and dynamics. It is subdivided into three parts covering relatively broad topics: (1) molecular structure and modeling, inclusive of current problems and state of computation (Chapters 1-6); (2) molecular mechanics: force field origin, composition, and evaluation techniques (Chapters 7-9); and (3) simulation techniques: conformational sampling by geometry optimization, Monte Carlo, and molecular dynamics approaches (Chapter 10-13). The last chapter (Chapter 14) is devoted to discussing the similarity and diversity problems in chemical design. The book's appendices complement the material in the main text through homework assignments, reading lists, and other information useful for teaching molecular modeling.\par The book is intended for students of an interdisciplinary graduate course in molecular modeling as well as for researchers (physicists, mathematicians and engineers) to get them started in computational molecular biology."

"Molecular modeling … is now an important branch of modern biochemistry. … Schlick has brought her unique interdisciplinary expertise to the subject. … One of the most distinguished characteristics of the book is that it makes the reading really fun … and the material accessible. … a crystal clear logical presentation … . Schlick has added a unique title to the collection of mathematical biology textbooks … . a valuable introduction to the field of computational molecular modeling. It is a unique textbook … ." (Hong Qian, SIAM Reviews, Vol. 47 (4), 2005)

"The text is beautifully illustrated with many color illustrations. Even part of the text is typeset in color. Not only the illustrations interrupt the very readable text, there are also many box-insertions … . So, if you read this as a teacher, you will find enough material to build your own lecture notes for your own group of students. To conclude, this is a broad and relaxed introduction to the field of molecular modeling." (Adhemar Bultheel, Bulletin of the Belgian Mathematical Society, Vol. 11 (4), 2004)

"This textbook evolved from a graduate course in molecular modeling, and was expanded to serve as an introduction to the field for scientists in other disciplines. … The book is unique in that it combines introductory molecular biology with advanced topics in modern simulation algorithms … . the author provides 1000+ references, and additionally includes reading lists complementing the main text. This is an excellent introductory text that is a pleasure to read." (Henry van den Bedem, MathSciNet, September, 2004)

"This book provides an excellent introduction to the modeling of biomolecular structures and dynamics. … The book’s appendices complement the material in the main text through homework assignments, reading lists, and other information useful for teaching molecular modeling. The book is intended for students of an interdisciplinary graduate course in molecular modeling as well as for researchers (physicists, mathematicians and engineers) to get them started in computational molecular biology." (Ivan Krrivý, Zentralblatt MATH, Issue 1011, 2003)

"The book … is the outcome of the author Tamar Schlick’s teaching experience at New York University. It is a fantastic graduate textbook to get into structural biology. … even the most sophisticated problems are part of a gradual approach … . The book will obviously be of great interest to students and teachers but it should also be very valuable for research scientists, especially newcomers to the field … as a reference book and a point of entry in the more specialised literature." (Benjamin Audit, Bioinformatics, January, 2003)

"The basic goal of this new text is to introduce students to molecular modelling and simulation and to the wide range of biomolecular problems being attacked by computational techniques. … the text emphasises that the field is changing very rapidly and that it is full of exciting discoveries. … This book stimulates this excitement, while still providing students many computational details. … It contains detailed illustrations throughout ... . It should appeal to beginning graduate students … in many scientific departments ... ." (Biotech International, Vol. 15 (2), 2003)

Product Details

• Hardcover: 656 pages
• Publisher: Springer; 1 edition (August 19, 2002)
• Language: English
• ISBN-10: 038795404X
• ISBN-13: 978-0387954042
• Product Dimensions: 9 x 6.9 x 1.5 inches
• Shipping Weight: 2.4 pounds
• Average Customer Review: 4.8 out of 5 stars  See all reviews (12 customer reviews)
• Amazon Best Sellers Rank: #394,915 in Books (See Top 100 in Books)
  • #12 in Books > Professional & Technical > Professional Science > Chemistry > Molecular Chemistry
  • #66 in Books > Professional & Technical > Professional Science > Biological Sciences > Biophysics

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Customer Reviews

Most Helpful Customer Reviews

7 of 7 people found the following review helpful:

5.0 out of 5 stars Outstanding introduction, May 13, 2004

By 

wiredweird "wiredweird" (Earth, or somewhere nearby) - See all my reviews
(HALL OF FAME REVIEWER)    (TOP 500 REVIEWER)   

This review is from: Molecular Modeling and Simulation (Hardcover)

... 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.

9 of 10 people found the following review helpful:

5.0 out of 5 stars A long expected book in molecular modeling is finally here, February 16, 2004

By 

Javier Arsuaga (San Francisco, CA, USA) - See all my reviews

This review is from: Molecular Modeling and Simulation (Hardcover)

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.

4 of 4 people found the following review helpful:

5.0 out of 5 stars Gateway to molecular simulation, August 4, 2003

By 

Jesus A Izaguirre (Notre Dame, Indiana United States) - See all my reviews

This review is from: Molecular Modeling and Simulation (Hardcover)

"Molecular Modeling and Simulation: An Interdisciplinary Guide" is an excellent entry point to this subject. It is suitable as a reference for research on methods for molecular modeling, and as a textbook. For example, I have used it both as a reference for the development of new computational methods and as a textbook on an introductory graduate/advanced undergraduate seminar on computational biology. The introductory material is superb, introducing experimental and theoretical developments in understanding proteins (chapters 1-4) and nucleic acids (chapters 5,6). This material is particularly useful to computer scientists, mathematicians, or physicists who want to understand the problems addressed by biomolecular simulations, such as protein folding. The material is up to date, clearly presented, and beautifully illustrated with simulation results. In our course, students gave presentations on each one of these chapters, and all found the material accessible, and the references therein valuable to expand on details.

The most original material of this book is the discussion of computational methods for biomolecular simulation. After an excellent introduction in chapter 7, the book covers force fields (the description of the interacting forces in a biomolecule) in chapter 8, fast n-body solvers for electrostatic computation in chapter 9, optimization methods in chapter 10, and Monte Carlo (chapter 11) and molecular dynamics (chapters 12,13). The author has made notable contributions in these areas, and presents an advanced body of knowledge in a precise and consistent manner. An added benefit is that she frequently accompanies the mathematical descriptions by simulation results using the methods, and gives substantial references that allow the reader to assess the importance of the techniques discussed. As an instructor, I presented introductory material that is assumed in the book, to make it easier for the students to grasp the relevance of the more advanced material. There is also a final chapter on computer-assisted drug design, which is interesting, but somewhat unrelated to the rest of the material, since it focuses on techniques more statistical in nature.

Finally, the homework and sample syllabus provided as appendices in the book make the concepts accessible and relevant. In summary, this should be the book of choice for anyone desiring to go in depth into biomolecular modeling. Given the rapid advance of the field, I hope already for subsequent editions!