My 25 Years in CSIR and in My 25 Years in CSIR and in BioinformaticsBioinformatics

G P S RaghavaInstitute 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 My 25 Years in BioinformaticsBioinformatics

IMTECH is one of original DIC’s started by DBTIMTECH is one of original DIC’s started by DBT I start my carrier in 1986 as computer scientistI start my carrier in 1986 as computer scientist My first task was to support DIC at IMTECHMy first task was to support DIC at IMTECH 1986-91: Infrastructure (Email, NICNET, 1986-91: Infrastructure (Email, NICNET,

Medline)Medline) 1991-1996: Services with development of 1991-1996: Services with development of

computer programscomputer programs 1996-2001: Data based discovery, protein 1996-2001: Data based discovery, protein

structure, webstructure, web 2001-2006: Drug/Vaccine targets and genome 2001-2006: Drug/Vaccine targets and genome

annotationannotation 2006-2011: Integration of tools & collaboration2006-2011: Integration of tools & collaboration 2011-2016 ?: Drug/Vaccine in real life2011-2016 ?: Drug/Vaccine in real life

1986-91: Infrastructure & 1986-91: Infrastructure & ServicesServices

Literature searchLiterature search DIALOG search via TelexDIALOG search via Telex

MicroVax II (First powerful computer)MicroVax II (First powerful computer) Nucleotide and Sequence data on tapesNucleotide and Sequence data on tapes NICNET connectivity and databases NICNET connectivity and databases

searchessearches Email-Facility via ERNET (UUCP)Email-Facility via ERNET (UUCP) Email via NICNET to other DICsEmail via NICNET to other DICs EMBL data and software via Email EMBL data and software via Email

ServersServers

1991-1996: Advance level of 1991-1996: Advance level of serviceservice

Software development for biological Software development for biological problemsproblems

First research publication (1991)First research publication (1991) Number of publicationsNumber of publications Establishment of INTERNETEstablishment of INTERNET Completed Ph.D. (1996)Completed Ph.D. (1996)

1996-2001: International 1996-2001: International PresencePresence

Methods developed for protein structure Methods developed for protein structure predictionprediction

Participated in International competition Participated in International competition CASPCASP

Worked at Oxford University, UK (1996-Worked at Oxford University, UK (1996-1998)1998)

Mirror-Sites of software archievesMirror-Sites of software archieves

Web based applications launchedWeb based applications launched

2001-2006: Drug/Vaccine targets and 2001-2006: Drug/Vaccine targets and genome annotationgenome annotation

Adaptive Immunity (Cellular Response) : Thelper Epitopes

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

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

Cytopred: for classification of Cytokines

BCIpep: A database of B-cell eptioes; ABCpred: for predicting B-cell epitopesALGpred: for allergens and IgE eptopes

HaptenDB: A datbase of haptens

PRRDB: A database of PRRs & ligands

Antibp: for anti-bacterial peptides

2001-2006: Drug/Vaccine targets and genome 2001-2006: Drug/Vaccine targets and genome annotationannotation

Genome AnnotationFTGpred: Prediction of Prokaryotic genesEGpred: Prediction of eukaryotic genesGeneBench: Benchmarking of gene findersSRF: 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 MethodsPSLpred: localization of prokaryotic proteinsESLpred: localization of Eukaryotic proteins

HSLpred: localization of Human proteinsMITpred: Prediction of Mitochndrial proteins

TBpred: Localization of mycobacterial proteins

Prediction of drugable proteinsNrpred: Classification of nuclear receptorsGPCRpred: Prediction of G-protein-coupled receptorsGPCRsclass: Amine type of GPCR VGIchan: Voltage gated ion channelPprint: RNA interacting residues in proteinsGSTpred: Glutathione S-transferases proteins

Protein Structure PredictionAPSSP2: protein secondary structure predictionBetatpred: Consensus method for -turns prediction Bteval: Benchmarking of -turns prediction BetaTurns: Prediction of -turn types in proteins Turn Predictions: Prediction of / / -turns in proteinsGammaPred: 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/