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
TOC:
- 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
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