Transcript Role of Bioinformatics Tools in Biological Research G. P

My 25 Years in CSIR and in
Bioinformatics
G P S Raghava
Institute of Microbial Technology
Sector 39A, Chandigrah, India
Email: [email protected]
Web: http://www.imtech.res.in/raghava/
http://crdd.osdd.net/
My 25 Years in Bioinformatics
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IMTECH is one of original DIC’s started by DBT
I start my carrier in 1986 as computer scientist
My first task was to support DIC at IMTECH
1986-91: Infrastructure (Email, NICNET, Medline)
1991-1996: Services with development of computer
programs
1996-2001: Data based discovery, protein structure, web
2001-2006: Drug/Vaccine targets and genome
annotation
2006-2011: Integration of tools & collaboration
2011-2016 ?: Drug/Vaccine in real life
1986-91: Infrastructure & Services
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Literature search
 DIALOG search via Telex
MicroVax II (First powerful computer)
Nucleotide and Sequence data on tapes
NICNET connectivity and databases searches
Email-Facility via ERNET (UUCP)
Email via NICNET to other DICs
EMBL data and software via Email Servers
1991-1996: Advance level of service
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Software development for biological problems
First research publication (1991)
Number of publications
Establishment of INTERNET
Completed Ph.D. (1996)
1996-2001: International Presence
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Methods developed for protein structure
prediction
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Participated in International competition CASP
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Worked at Oxford University, UK (1996-1998)
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Mirror-Sites of software archieves
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Web based applications launched
2001-2006: Drug/Vaccine targets and genome
annotation Propred: for promiscuous MHC II binders
Adaptive Immunity
(Cellular Response) :
Thelper Epitopes
MMBpred:for high affinity mutated binders
MHC2pred: SVM based method
MHCBN: A database of MHC/TAP binders
and non-binders
Pcleavage: for proteome cleavage sites
Adaptive Immunity
(Cellular Response) :
CTL Epitopes
Adaptive Immunity
(Humoral Response)
:B-cell Epitopes
Innate Immunity :
Pathogen Recognizing
Receptors and ligands
Signal transduction in
Immune System
TAPpred: for predicting TAP binders
Propred1: for promiscuous MHC I binders
CTLpred: Prediction of CTL epitopes
BCIpep: A database of B-cell eptioes;
ABCpred: for predicting B-cell epitopes
ALGpred: for allergens and IgE eptopes
HaptenDB: A datbase of haptens
PRRDB: A database of PRRs & ligands
Antibp: for anti-bacterial peptides
Cytopred: for classification of Cytokines
2001-2006: Drug/Vaccine targets and genome
annotation
Comparative genomics
Genome Annotation
FTGpred: Prediction of Prokaryotic genes
EGpred: Prediction of eukaryotic genes
GeneBench: Benchmarking of gene finders
SRF: Spectral Repeat finder
Subcellular Localization Methods
PSLpred: localization of prokaryotic proteins
ESLpred: localization of Eukaryotic proteins
HSLpred: localization of Human proteins
MITpred: Prediction of Mitochndrial proteins
TBpred: Localization of mycobacterial proteins
GWFASTA: Genome-Wide FASTA Search
GWBLAST: Genome wide BLAST search
COPID: Composition based similarity search
LGEpred: Gene from protein sequence
Prediction of drugable proteins
Nrpred: Classification of nuclear receptors
GPCRpred: Prediction of G-protein-coupled receptors
GPCRsclass: Amine type of GPCR
VGIchan: Voltage gated ion channel
Pprint: RNA interacting residues in proteins
GSTpred: Glutathione S-transferases proteins
Protein Structure Prediction
APSSP2: protein secondary structure prediction
Betatpred: Consensus method for -turns prediction
Bteval: Benchmarking of -turns prediction
BetaTurns: Prediction of -turn types in proteins
Turn Predictions: Prediction of / / -turns in proteins
GammaPred: Prediction of-turns in proteins
BhairPred: Prediction of Beta Hairpins
TBBpred: Prediction of trans membrane beta barrel proteins
SARpred: Prediction of surface accessibility (real accessibility)
PepStr: Prediction of tertiary structure of Bioactive peptides
Important Points for CSIR Scientists
1. Why we join CSIR? (survival, Job, Recognition, service)
2. Are we lucky persons? ( Job security, environment)
3. Can anybody force us to work or not to work?
4. What is ultimate goal? (getting promotion on time, director)
5. What is level of competition? (lab, national, international)
6. Is scientist loyal to boss/director, institute, country, science?
7. Do we feel pride in front of our kids?
8. Are we liability on our institute/country?
9. Can I survive in competitive world (private, abroad)
10. Am I enjoying my life?
URLs: http://www.imtech.res.in/raghava/ & http://crdd.osdd.net/ & bic.uams.edu/