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My 25 Years in CSIR and in Bioinformatics

My 25 Years in CSIR and in Bioinformatics. G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah, India. Email: Raghava@imtech.res.in Web: http://www.imtech.res.in/raghava/ http://crdd.osdd.net/. My 25 Years in Bioinformatics.

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My 25 Years in CSIR and in Bioinformatics

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  1. My 25 Years in CSIR and in Bioinformatics G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah, India Email: Raghava@imtech.res.in Web: http://www.imtech.res.in/raghava/http://crdd.osdd.net/

  2. My 25 Years in Bioinformatics • 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

  3. 1986-91: Infrastructure & Services • 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

  4. 1991-1996: Advance level of service • Software development for biological problems • First research publication (1991) • Number of publications • Establishment of INTERNET • Completed Ph.D. (1996)

  5. 1996-2001: International Presence • Methods developed for protein structure prediction • Participated in International competition CASP • Worked at Oxford University, UK (1996-1998) • Mirror-Sites of software archieves • Web based applications launched

  6. 2001-2006: Drug/Vaccine targets and genome annotation Adaptive Immunity (Cellular Response) : Thelper Epitopes Propred: for promiscuous MHC II binders 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 TAPpred: for predicting TAP binders Propred1: for promiscuous MHC I binders CTLpred: Prediction of CTL epitopes Adaptive Immunity (Cellular Response) : 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 Adaptive Immunity (Humoral Response) :B-cell Epitopes Innate Immunity : Pathogen Recognizing Receptors and ligands PRRDB: A database of PRRs & ligands Antibp: for anti-bacterial peptides Signal transduction in Immune System Cytopred: for classification of Cytokines

  7. 2001-2006: Drug/Vaccine targets and genome annotation Genome Annotation FTGpred: Prediction of Prokaryotic genes EGpred: Prediction of eukaryotic genes GeneBench: Benchmarking of gene finders SRF: Spectral Repeat finder Comparative genomics GWFASTA:Genome-Wide FASTA Search GWBLAST: Genome wide BLAST search COPID: Composition based similarity search LGEpred: Gene from protein sequence 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 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

  8. Important Points for CSIR Scientists Why we join CSIR? (survival, Job, Recognition, service) Are we lucky persons? ( Job security, environment) Can anybody force us to work or not to work? What is ultimate goal? (getting promotion on time, director) What is level of competition? (lab, national, international) Is scientist loyal to boss/director, institute, country, science? Do we feel pride in front of our kids? Are we liability on our institute/country? Can I survive in competitive world (private, abroad) Am I enjoying my life?

  9. Thanku URLs: http://www.imtech.res.in/raghava/ & http://crdd.osdd.net/ & bic.uams.edu/

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