Bioinformatics: A Primer

261 Pages·2006·5.03 MB·English

by  P Narayanan

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Copyright © 2005, New Age International (P) Ltd., Publishers
Published by New Age International (P) Ltd., Publishers
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Dedicated to my parents, in their
memory, and to my wife and son,
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Preface
Associations of elements, molecules, their complexes and aggregates have physicochemical
information content that would be of chemical and biological importance. Therefore, there is
tendency to address wide varieties of physicochemical interactions under “Bioinformatics”.
Such an approach would unfortunately dilute the focus of the main objectives of bioinformatics.
“Bioinformatics” is the study (by experimental and computational) of biological informa-
tion, from its storage sites (DNA/RNA) in the genome to the various gene products in the cell.
In the case of life processes, to the realm of which bioinformatics logically belongs, the funda-
mental building blocks that the life systems made up are nucleic acids, proteins, carbohy-
drates, lipids and their complexes. The central aims of bioinformatics, therefore, is to elucidate
(by experimental methods) and understand structural (primary, secondary, tertiary etc.) fea-
tures of these biological entities and correlate these structural features to address the physico-
chemical interactions, functions and pathways among these molecular entities in the cell
(experimentally as well as computationally).
Bioinformatics is a multi-disciplinary subject, with immense scope in molecular biology,
biotechnology, pharmaceutical and medical fields– e.g., genome and protein sequencing,
structure prediction and molecular modeling and drug design and development of novel
molecules and drugs (molecular engineering), medical diagnostics and therapeutics. With the
advances in experimental methodologies (X-ray diffraction; NMR spectroscopy) in molecular
structure determination, biology has become data-rich with considerable amount of experi-
mental data being made available on complex biomolecular structures. Tremendous progress
in computational arenas has also been taking place, in terms of vast data storage capacity,
processing and visual display. These developments have made it possible to address complex
array of biological systems and interactions in a systematic and quantitative way.
Study of bioinformatics as understood and pursued (by computational and biomedical
scientists) is treated with computational biology, which relies primarily on computational
(theoretical) methods as applied to biological and medical sciences–in areas such as in genomics,
proteomics, drug design etc. In this kind of approach there is a tendency to underplay the
crucial importance of experimental methods of data acquisition and structure-function inter-
pretation. But, the availability of structural data by experimental methods is the core aspect in
rational molecular drug design (molecular engineering) and validation. Lack of such data or
viii Preface
poor understanding would lead to spurious and inconsistent molecular models and thus
would undermine the very objective of bioinformatics.
The major objectives of bioinformatics still are the same–
(i) Development of computer databases and algorithms to analyze biological data.
(ii) Processing, and interpretation of these complex physicochemical databases on molecu-
lar interactions, structures and functions of biomolecules.
(iii) Computational methods for structure prediction and molecular modeling (molecular
engineering/drug design), based on available experimental data that include cases
where the existing experimental techniques are too time-consuming, or unable to pro-
vide structural information due to inherent operational constraints.
Till recently, progress in bioinformatics (quantitative biology) was initiated and nurtured by
physical scientists (crystallographers; NMR specialists) and biologists. However, this situation
is changing with bioinformatics relying more and more upon computation-oriented problem-
solving protocols. Biologists may know biological systems and their functions, but the empha-
sis should be, while taking up computational bioinformatics, on the structural and functional
aspects of biological molecules vis a vis their physical and chemical characteristics. On the
other hand, the computational personnel may be versatile in the operational aspects of com-
puter programs and algorithms, but the real handicap arises if they lack basic knowledge
about the structures and functions of biological systems, whose complexity they are supposed
to unravel. This situation is akin to a driver who is adept at driving automobiles but lacks the
basic knowledge of automobile engineering. Therefore, it is imperative that both groups have
operational knowledge of the essentials of molecular biophysics, molecular biochemistry and
structural biology while undertaking the task of molecular modeling and design.
With these broad objectives in mind, the material contents of this book, “Bioinformatics: A
Primer”, are organized under molecular biophysics, experimental methods of structure eluci-
dation, database search, data mining and analysis, computational methods of structure pre-
diction, and rational molecular/drug design and validation, with easy interface between these
areas and various chapters. Ample tables and figures, culled form the Protein Data Bank (PDB)
and other sources, are intended to facilitate the reader insights to the structure-function
features at the molecular level. Exercise modules and bibliography for each chapter, and
glossary are aimed at providing the reader wider perception and insight to the subject matter,
and scientific and technical terms. Index is also provided to help in easy access to the words
and topics to the subject matter.
P. Narayanan
Acknowledgement
Thanks are due to Ms. Swarna Murthy, Bhabha Atomic Research Centre, Mumbai, for
rendering bibliographic help.
P. Narayanan