Molecular Modeling and Simulation: An Interdisciplinary Guide


Author(s): Tamar Schlick

During the past two decades biological sciences experienced a revolution with the explosion of computational approaches for molecular biology and it has become clear that in silico analysis was essential to broaden our point of view in this research field. Major breakthroughs have paved the way in topics like sequence analysis, molecular databases, protein and nucleic acids structure prediction or molecular evolution. What is now called Bioinformatics or Computational Biology took shape as an independent discipline and gained the right to be taught as such in universities. The book Molecular Modeling and Simulation 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. 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. Also, the book reviews the state of the art in biological macromolecule modeling and simulation, and introduces the current problems and perspectives in structural biology. The main text is accompanied by a large number of colour illustrations and boxed texts that highlight a particular achievement or technique, and by an impressive reference list with 1009 entries. A series of appendices provide further material for teaching purposes including some selected references of articles and textbooks.

Due to the interdisciplinary nature of structural biology, the topics to be covered are very diverse going from biochemistry to theoretical physics and numerical methods, yet this diversity is not the source of confusion. Indeed, the author organised the book in a clear progressive fashion that steadily takes us from the geometrical description of macromolecules to the simulation of their dynamics. The first two chapters play the role of an introduction: chapter one provides a wide historical overview including related fields of research such as crystallography and chapter two presents the scientific and social motives for molecular modeling through compelling examples e.g. the folding problem (prion diseases, chaperon complexes) or drug design (AIDS).The rest of the book is clearly divided between two types of chapters: the first type is devoted to basic knowledge while the second type deals with more advanced developments. Starting from a presentation of the biochemical constituents and the spatial conformations of protein and nucleic acids, the book leads us to a description of the physical principles and forces that govern the interaction between atoms. Then, the problem of modeling these interactions is tackled and in particular the necessary trade off between computational resources and the accuracy of the physical models. From this point on, simulation techniques are described: minimisation and Monte Carlo methods that are useful to estimate equilibrium conformations and thermodynamic functions, followed by proper molecular dynamics approaches. Finally, the last chapter is devoted to small chemical compounds and problems in chemical design.

The main achievement of the book is that even the most sophisticated problems are part of a gradual approach, maybe too scholar from time to time but certainly efficient. I would only regret some imprecisions in the introductory part of the book. For example, it is not fair to highlight the achievements of GENBANK without citing its European (EMBL databank) and Japanese (DDBJ) counterparts, the work of the British two times Nobel Prize winner Fred Sanger is not cited in the historical perspective and his last name is not spelt correctly. 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 specialised literature.

Benjamin Audit: EBI, UK


  • Biomolecular Structure and Modeling: Historical Perspective
  • Biomolecular Structure and Modeling: Problem and Application Perspective
  • Protein Structure Introduction
  • Protein Structure Hierarchy
  • Nucleic Acids Structure Minitutorial
  • Topics in Nucleic Acids Structure
  • Theoretical and Computational Approaches to Biomolecular Structure
  • Force Fields
  • Nonbonded Computations
  • Multivariate Minimization in Computational Chemistry
  • Monte Carlo Techniques
  • Molecular Dynamics: Basics
  • Molecular Dynamics: Further Topics
  • Similarity and Diversity in Chemical Design
  • Epilogue
  • Appendices
  • Index

Hardcover, 656 pages, 147 illus.; Textbook, published 2002; Springer-Verlag