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Bioinformatics Drug Informatics Vaccine Informatics Chemoinformatics

Knowledge based Drug Design & Open source Web Services. Dr G P S Raghava, Head Bioinformatics Centre. Institute of Microbial Technology, Chandigarh, India. Bioinformatics Drug Informatics Vaccine Informatics Chemoinformatics. Email: raghava@imtech.res.in http://crdd.osdd.net/

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Bioinformatics Drug Informatics Vaccine Informatics Chemoinformatics

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  1. Knowledge based Drug Design & Open source Web Services Dr G P S Raghava, Head Bioinformatics Centre Institute of Microbial Technology, Chandigarh, India Bioinformatics Drug Informatics Vaccine Informatics Chemoinformatics Email: raghava@imtech.res.inhttp://crdd.osdd.net/ http://www.imtech.res.in/raghava/

  2. Exponential Growth of Data: Source of Knowledge

  3. Example of Open Source Resources • Operating Systems • Linux • FreeBSD, OpenBSD, and NetBSD • Internet • Apache (> 50% of the world's web servers) • BIND: DNS for the entire Internet. • Sendmail (Most email servers) • OpenSSL (standard for secure communication) • Programming Tools • Languages (Perl, Python, PHP) • GNU compilers and tools (GCC, Make)

  4. Open source Web Services

  5. OSDDLINUX Customized operating environment for drug discovery pipeline Bioinformatics VACCINE Informatics Pkg Repository Live CD ChemInformatics Live Server Installation Standalone Webserver Galaxy platform All in ONE

  6. Drug/inhibitor/vaccine/ Disease Diagnostics Peptide-Protein Interaction Peptide Structure, docked structure Adaptive Immunity: B-cell, T-cell Epitope Innate Immunity: Toll-like receptors Anti-(bacterial , microbial, cancer, viral) peptides Mimotopes for diseases diagnostics Structure determination: Natural, non-natural , modified bonds Structure prediction: Natural, non-natural , modified bonds Peptide/ Proteins Synthesis: Phase display, SPSS, Codon Suffeling Natural bioactive peptides from metagenomics Mimotopes for B/T epitopes Mimicking of Drug Molecules Size Optimization for function/Str. ADMET: Proteolytic enzymes, Half-life Oral Delivery : Trans. & Adjuvant

  7. Adaptive Immunity Protective Antigens Vaccine Informatics Bioinformatics Centre Innate Immunity IMTECH, Chandigarh Vaccine Delivery Purified Antigen WHOLE ORGANISM Epitopes (Subunit Vaccine) T cell epitope Attenuated

  8. Adaptive Immunity Protective Antigens Vaccine Informatics Bioinformatics Centre Disease Causing Agents Innate Immunity IMTECH, Chandigarh Vaccine Delivery Pathogens/Invaders

  9. Modelling of Immune System for Designing Epitope-based Vaccines 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

  10. Designing of therapeutic peptides against cancer Anticancer peptides AntiCP Peptide inhibitors DipCells Cell Penetrating Peptides: CPPsite; CellPPD Tumor Homing Peptides TumorHoPe; TumorHPD ? Peptides Half-life HLP Toxicity of Peptides ToxinPred

  11. Peptide Resources/Databases Work in Progress 1. Prediction of CPP 2. Designing CPP 3. Scanning in proteins

  12. Peptide Resources/Databases Work in Progress 1. Prediction of CPP 2. Designing CPP 3. Scanning in proteins

  13. Peptide Resources/Databases

  14. Peptide Web Servers

  15. Peptide Web Servers

  16. Designing of antibacterial stable peptides Scanning of peptides in a protein Submition of multiple peptides

  17. Thank You http://www.imtech.res.in/raghava/

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