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Introduction and Importance of Bioinformatics
Application in Drug/Vaccine Design G. P. S.
Raghava Email raghava_at_imtech.res.in Web
http//www.imtech.res.in/raghava/
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What is Bioinformatics (BI) ? Historical
Background Why Bioinformatics is RequiredCore
of BioinformaticsImportant Applications of BI
Future Prospectus of Bioinformatics
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Bioinformatics mines data
Db
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What is Bioinformatics

• Biocomputing Application of Computer in
  Biosciences
• Biocomputing started in 1960s
• Explosion of Genomic Data
• Access and Management of Data
• BiocomputingInformation Science
• Role of Internet in BI

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Brief History

• 1953 DNA structure discovered
• 1960 Assembly of protein sequence database - PIR
• 1977 Sanger sequencing technique developed
• 1979 GenBank prototype was conceived
• 1980 EMBL database was founded
• 1988 Human Genome project initiated
• 1993 The first genome database ACEDB (C. elegans)
• 1995 Influenza genome sequenced (5Mb)
• 1998 High throughput sequencing machine
  developed by PE Biosystems
• 2000 Drosophila genome sequenced (180Mb)
• 2001 Human genome rough draft (2.91Bb)

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Why Bioinformatcs is Required

• Data growth is exponential
• Difficult to understand life without BI
• Detection of new diseases
• BI tools allow to save expr. Expend.
• Rational Drug design
• Computer-aided vaccine design

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GOLDGenome Online Database Published Complete
Genomes 93 - 16 Archaeal - 65 Bacterial - 12
Eukaryal On-going - Prokaryotes 284 -
Eukaryotes 195 Last update 17 June 2002
(1439hrs) Kyrpides, N. (1999) Bioinformatics 15,
773-774 wit.integratedgenomics.com/GOLD/
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Growth of Swiss prot
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Growth of PDB
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Growth of gene-driven research
One paper every five minutes
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Application of Bioinformatics

• Genome Annotation
• Protein Structure Prediction
• Proteomics
• DNA Chip technology
• Disease Diagnostics
• Fingerprinting Technique
• Drug/Vaccine Design

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Genome Annotation

• The Process of Adding Biology Information and
• Predictions to a Sequenced Genome Framework

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Protein Structures

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Protein Structure Prediction

• Experimental Techniques
• X-ray Crystallography
• NMR
• Limitations of Current Experimental Techniques
• Protein DataBank (PDB) -gt 17000 protein
  structures
• SwissProt -gt 90,000 proteins
• Non-Redudant (NR) -gt 800,000 proteins
• Importance of Structure Prediction
• Fill gap between known sequence and structures
• Protein Engg. To alter function of a protein
• Rational Drug Design

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Traditional Proteomics

• 1D gel electrophoresis (SDS-PAGE)
• 2D gel electrophoresis
• Protein Chips
• Chips coated with proteins/Antibodies
• large scale version of ELISA
• Mass Spectrometry
• MALDI Mass fingerprinting
• Electrospray and tandem mass spectrometry
• Sequencing of Peptides (N-gtC)
• Matching in Genome/Proteome Databases

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Fingerprinting Technique

• What is fingerprinting
• It is technique to create specific pattern for a
  given organism/person
• To compare pattern of query and target object
• To create Phylogenetic tree/classification based
  on pattern
• Type of Fingerprinting
• DNA Fingerprinting
• Mass/peptide fingerprinting
• Properties based (Toxicity, classification)
• Domain/conserved pattern fingerprinting
• Common Applications
• Paternity and Maternity
• Criminal Identification and Forensics
• Personal Identification
• Classification/Identification of organisms
• Classification of cells

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Bioinformatics Approach for Identification of
Vaccine Candidate

• Identification of the vaccine candidates
  (Antigenic Region) for designing subunit vaccine.
• Antigen degraded in peptides by proteasome
• MHC Molecule bind to antigenic peptide
• MHCpeptide to cell surface
• Prediction of Promiscuous MHC binding peptides.
• Prediction Method for T-Cell Epitopes.
• Molecular Mimicry
• Model Studies on HIV and M.tuberculosis

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Drug Design based on Bioinformatics Tools

• Detect the Molecular Bases for Disease
• Detection of drug binding site
• Tailor drug to bind at that site
• Protein modeling techniques
• Traditional Method (brute force testing)
• Rational drug design techniques
• Screen likely compounds built
• Modeling large number of compounds (automated)
• Application of Artificial intelligence
• Limitation of known structures
• Search of Target protein
• Search of Lead compound

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Steps in Post-Genomics
? Transcriptomics large-scale analysis of
messenger RNAs when, where, and under what
conditions genes are expressed. ? Proteomics
study of protein expression in time and space,
more important than gene expression studies
to whats actually happening in the cell. ?
Structural genomics 3-D structures of one or
more proteins from each protein family, clues
to function and biological targets for drug
design. ? Knockout studies experimental method
for understanding the function of DNA
sequences and the proteins they encode.
Inactivate genes in living organisms and
monitor any changes, reveal the function of
specific genes. Majority of knockouts do not give
null phenotype.   ? Comparative genomics DNA
sequence patterns of humans and well-studied
model organisms, most powerful strategies for
identifying human genes and interpreting their
function.
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Business Opportunities in BI

• Software development
• Web servers development
• Train manpower in Field of BI
• Database management
• Rational Drug design
• Develop Diagnostic kits
• Assist user in Vaccine development
• Consultant to Biotech Companies

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THANK YOU!