BioinformaticsDrug InformaticsVaccine Informatics Chemoinformatics

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Presentation transcript:

BioinformaticsDrug InformaticsVaccine Informatics Chemoinformatics Knowledge based Drug Design & Open source Web Services Institute of Microbial Technology, Chandigarh, India

Exponential Growth of Data: Source of Knowledge

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 servers) – OpenSSL (standard for secure communication) Programming Tools – Languages (Perl, Python, PHP) – GNU compilers and tools (GCC, Make)

Open source Web Services

Live CD Installation Standalone Webserver Galaxy platform All in ONE Live Server Pkg Repository

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

Innate ImmunityVaccine Delivery Protective AntigensAdaptive Immunity Bioinformatics Centre IMTECH, Chandigarh WHOLE ORGANISM Attenuated Epitopes (Subunit Vaccine) Purified Antigen T cell epitope

Pathogens/Invaders Disease Causing Agents Innate ImmunityVaccine Delivery Protective AntigensAdaptive Immunity Bioinformatics Centre IMTECH, Chandigarh

Modelling of Immune System for Designing Epitope-based Vaccines Adaptive Immunity (Cellular Response) : T helper 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 epitopes ALGpred: for allergens and IgE eptopes HaptenDB: A datbase of haptens PRRDB: A database of PRRs & ligands Antibp: for anti-bacterial peptides

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

Peptide Resources/Databases Work in Progress 1. Prediction of CPP 2. Designing CPP3. Scanning in proteins

Peptide Resources/Databases Work in Progress 1. Prediction of CPP 2. Designing CPP3. Scanning in proteins

Peptide Resources/Databases

Peptide Web Servers

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