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Bioinformatics Drug Informatics Vaccine InformaticsChemoinformatics
Email: [email protected] http://crdd.osdd.net/
http://www.imtech.res.in/raghava/
Email: [email protected] http://crdd.osdd.net/
http://www.imtech.res.in/raghava/
Knowledge based Drug Design & Open source Web Services
Institute of Microbial Technology, Chandigarh, India
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Exponential Growth of Data: Source of Knowledge
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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)
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Open source Web Services
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Live CDLive CD
InstallationInstallation
StandaloneStandaloneWebserverWebserver Galaxy platformGalaxy platform All in ONEAll in ONE
Live ServerLive Server
Pkg RepositoryPkg Repository
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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 epitopes Mimicking of Drug Molecules
ADMET: Proteolytic enzymes, Half-life
Oral Delivery : Trans. & Adjuvant
Size Optimization for function/Str.
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Innate Immunity Vaccine Delivery
Protective AntigensAdaptive Immunity
Bioinformatics CentreIMTECH, Chandigarh
WHOLEORGANISM
Attenuated
Epitopes (Subunit Vaccine)
Purified Antigen
T cell epitope
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Pathogens/Invaders
Disease Causing Agents
Innate Immunity Vaccine Delivery
Protective AntigensAdaptive Immunity
Bioinformatics CentreIMTECH, Chandigarh
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Modelling of Immune System for Designing Epitope-based Vaccines
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
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Designing of therapeutic peptides against cancer
Anticancer peptides AntiCP Peptide inhibitors DipCells
Cell Penetrating Peptides: CPPsite; CellPPD ?
Tumor Homing Peptides TumorHoPe; TumorHPD
Peptides Half-lifeHLP
Toxicity of PeptidesToxinPred
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Peptide Resources/Databases
Work in Progress
1. Prediction of CPP 2. Designing CPP 3. Scanning in proteins
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Peptide Resources/Databases
Work in Progress
1. Prediction of CPP 2. Designing CPP 3. Scanning in proteins
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Peptide Resources/Databases
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Peptide Web Servers
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Peptide Web Servers
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Designing of antibacterial stable peptides
Scanning of peptides in a protein
Submition of multiple peptides
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