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Trends in Bioinformatics

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University of Madras. Outline of Presentation. What is Bioinformatics ? ... The content of this exemplary online course covers major areas of Bioinformatics ... – PowerPoint PPT presentation

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Title: Trends in Bioinformatics


1
Trends in Bioinformatics Computational
Biology(From Genomics To Proteomics)
  • Professor K. Sundaram, Ph.D.
  • Former Professor Head
  • Department of Crystallography Biophysics
  • University of Madras

2
Outline of Presentation
  • What is Bioinformatics ?
  • Why sudden spurt of interest recently ?
  • Scope for Services/Products/Solutions ?
  • What activities are possible ?
  • By Individual -- By Institution -- By
    Industry
  • By State -- By Country

3
What is Bioinformatics ?
  • The content of this exemplary online course
    covers major areas of Bioinformatics (as of early
    1990s)
  • Introduction to Biotechnology
  • Pairwise Sequence Alignments
  • Networking
  • Multiple Alignment
  • Molecular Phylogenetics
  • Protein Folding

4
Birds Eye View of Biotechnology
  • Every Bioinformatician must have some knowledge
    of the fields of Molecular Biology and
    Biotechnology
  • An effective and succinct coverage through
    annotated illustrations has been created by
    Access Excellence
  • Other such resources are also available on the
    Net
  • Efforts like these (that organizations or
    individuals can undertake) are also valuable
    contributions to Bioinformatics and Biotechnology

5
Computer Technology in Biotechnology
  • Computer hardware and software tools are
    integral parts of most biotechnological
    procedures - see e.g., this review of 1997
  • The recent spurt in bioinformatics has resulted
    from the sequencing of all the genes in the
    entire human genome (see The Human Genome
    Project)
  • The whole genome of the following species have
    also been sequenced e-coli, yeast, mouse,
    mosquito, rice
  • Many others are in the pipeline
  • IT is indispensable if all these data have to be
    preserved and made available to researchers

6
Analysis of cDNA Microarray Data
  • Decoding of several genomes has spurred many new
    areas of intense research activity
  • One such is cDNA microarray technology
  • Biostatisticians and software professionals are
    sought after for the analysis of cDNA microarray
    data
  • Here is a sample of theory used to normalise cDNA
    microarray data
  • Theoretical prediction of the three dimensional
    structure of a protein, given its sequence, is
    another area that has attracted renewed interest
    in the postgenomic era

7
Protein Tertiary Structure Prediction
  • Completion of the HGP, an enormous achievement,
    marks none the less, just the biginning of a
    bigger challenge -- The quest to decode the
    Proteome
  • The base sequences in genes code for all the
    proteins.
  • Proteins are responsible for virtually all the
    functions of a living system
  • Activity of a protein is determined by its 3D
    structure
  • There is a strong belief that the native 3D
    structure of a protein is determined by its
    primary sequence (and hence the base sequence in
    the corresponding gene)
  • But the rules of the game are not yet fully
    understood

8
Ramachandran Plot
  • G.N. Ramachandran is credited with the discovery
    of a major first step in Protein Structure
    Prediction
  • The disposition of adjacent peptide units is
    restricted to a few allowed regions as shown in
    the adjoining Ramachandran (f, y) plot

9
PDB -- The Protein Data Bank
  • The PDB is a rather unique database, much sought
    after by protein structure predictors
  • Each PDB entry consists basically of the (x, y,
    z) coordinates of atoms in a protein determined
    experimentally (by x-ray crystallography or nmr)
  • Experimental determination of structure requires
    the protein in very pure form (near 100)
  • This was very difficult to achieve in early days
    but easier now, thanks to recombinant DNA
    technology
  • Similarly methods of structure solution have
    improved significantly due to advances in
    technology

10
PDB -- The Protein Data Bank (Contd.)
  • The PDB currently holds over 19,500 entries and
    the number keeps increasing rapidly
  • All the same, there is no hope of determining the
    3D structures of all the proteins of the proteome
  • This is the reason why 3D structure prediction
    methods have assumed a new significance
  • Various techniques are being explored to work out
    structures theoretically based on patterns
    observed in PDB proteins or ab initio using
    molecular physics

11
Protein Structure Prediction
  • CASP (Critical Assessment of Techniques for
    Protein Structure Prediction) is a competition
    organised every two years and makes an objective
    assessment of various prediction methods
  • CAFASP is a related activity where fully
    automated protein structure prediction servers
    are assessed
  • Organizers of CASP and CAFASP also conduct a
    community wide cooperative program, TMW, in an
    attempt to determine theoretically the structure
    of Ten Most Wanted proteins that are needed to
    solve scientific/ medical problems and for which
    there exists no hope of obtaining the structure
    experimentally in the near future

12
Protein Structure Prediction (Contd.)
  • Present day PCs have reached a stage that
    enables an individual to participate in these
    ventures effectively
  • The algorithm of such a program used to
    participate in the TMW effort is described below
  • An internal coordinates representation is used
    and standard planar geometry used for the peptide
    unit. With these assumptions a model of the
    protein can be simulated given its primary
    sequence
  • Cartesian coordinates of all the atoms are
    obtained looking at the molecule as a tree-like
    structure and moving from terminal atoms (leaves)
    towards the root atom and applying an affine
    transformation for each bond traversal (see next
    slide)

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14
Protein Structure Prediction (Contd.)
  • Starting conformation of a protein can be input
    in one of two forms
  • (1) As a sequence of single letter aminoacid
    codes and the local dipeptide conformations at
    each a carbon atom (see example)
  • (2) As a sequence of records, one for each
    residue. The record for each residue contains the
    residue name followed by the values of variable
    torsion angles f, y, and, cs (see example)
  • Total nonbonded energy is calculated using these
    formulae

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18
Protein Structure Prediction (Contd.)
  • Various strategies are used to generate likely
    conformations for the protein using a simulated
    annealing approach adopting the Monte Carlo
    algorithm
  • A more detailed description is available in this
    article

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20
Proteomics Research
  • Once the structure of a protein is obtained,
    further research can be carried out in areas like
    functional genomics and proteomics
  • Several proteins are suspected to engage in
    function related specific associations. This can
    be investigated theoretically as discussed in
    this article
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