Molecular Modeling and Simulation

1. Front Matter

   Pages i-xliii

   PDF

2. Biomolecular Structure and Modeling: Historical Perspective

   • Tamar Schlick

   Pages 1-32

3. Biomolecular Structure and Modeling: Problem and Application Perspective

   • Tamar Schlick

   Pages 33-60

4. Protein Structure Introduction

   • Tamar Schlick

   Pages 61-90

5. Protein Structure Hierarchy

   • Tamar Schlick

   Pages 91-112

6. Nucleic Acids Structure Minitutorial

   • Tamar Schlick

   Pages 113-146

7. Topics in Nucleic Acids Structure

   • Tamar Schlick

   Pages 147-198

8. Theoretical and Computational Approaches to Biomolecular Structure

   • Tamar Schlick

   Pages 199-224

9. Force Fields

   • Tamar Schlick

   Pages 225-258

10. Nonbonded Computations

    • Tamar Schlick

    Pages 259-304

11. Multivariate Minimization in Computational Chemistry

    • Tamar Schlick

    Pages 305-344

12. Monte Carlo Techniques

    • Tamar Schlick

    Pages 345-381

13. Molecular Dynamics: Basics

    • Tamar Schlick

    Pages 383-418

14. Molecular Dynamics: Further Topics

    • Tamar Schlick

    Pages 419-462

15. Similarity and Diversity in Chemical Design

    • Tamar Schlick

    Pages 463-496

16. Epilogue

    • Tamar Schlick

    Pages 497-497

17. Back Matter

    Pages 499-635

    PDF

Science is a way of looking, reverencing. And the purpose of all science, like living, which amounts to the same thing, is not the ac­ cumulation of gnostic power, the fixing of formulas for the name of God, the stockpiling of brutal efficiency, accomplishing the sadistic myth of progress. The purpose of science is to revive and cultivate a perpetual state of wonder. For nothing deserves wonder so much as our capacity to experience it. Roald Hoffman and Shira Leibowitz Schmidt, in Old Wine, New Flasks: Re. flections on Science and Jewish Tradition (W. H. Freeman, 1997). Challenges in Teaching Molecular Modeling This textbook evolved from a graduate course termed Molecular Modeling intro­ duced in the fall of 1996 at New York University. The primary goal of the course is to stimulate excitement for molecular modeling research - much in the spirit of Hoffman and Leibowitz Schmidt above - while providing grounding in the discipline. Such knowledge is valuable for research dealing with many practical problems in both the acadernic and industrial sectors, from developing treatments for AIDS (via inhibitors to the protease enzyme of the human imrnunodeficiency virus, HIV-1) to designing potatoes that yie1d spot-free potato chips (via trans­ genic potatoes with altered carbohydrate metabolism). In the course of writing xii Preface this text, the notes have expanded to function also as an introduction to the field for scientists in other disciplines by providing a global perspective into problems and approaches, rather than a comprehensive survey.

• Dynamics
• Monte Carlo
• Multivariat
• algorithms
• chemistry
• design
• mechanics
• modeling
• molecular biology
• optimization
• protein
• protein structure
• simulation
• visualization
• biochemical engineering

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 excitingdiscoveries. 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 incomputational 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 ofan 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)

• Department of Mathematics and Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, USA

  Tamar Schlick

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