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Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering IT related services (Facilities.

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Presentation on theme: "Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering IT related services (Facilities."— Presentation transcript:

1 Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering IT related services (Facilities for IMTECH) Research in Computational Biology Web Servers and Databases BIC @ IMTECH

2 Brief History of the Centre Established in 1987 by DBT Network between centres in 1989, via NICNET. EMAIL facility in 1990 under ERNET project. 1991: Research in Bioinformatics initiated 1994: Alpha Chips based high speed computer. Local Area Network was established in 1994. Internet & Intranet in was setup at IMTECH 1997. Research group in bioinformatics started in1998 Computing Ab/Ag concentration from ELISA data

3 Infrastructure for Molecular Modelling Hardware High Performance Clusters (> 10 Teraflops) –IBM 14 node, 28 core, P6 processos (Best for protein modelling) –SUN HPC/Webserver (160 core AMD), Best for webservices –Supercomputer 400 core of Xeon 3.2GHz (> 6 Teraflops) Bioinformatics cluster: 4 node Apple G5 cluster Workstations: SGI & DELL, SUN, HP graphics workstations Computers for proteins modelling: SGI, SUN, IBM and Digital servers IBM Cluster

4 Computer-Aided Drug Discovery Searching Drug Targets: Bioinformatics 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

5 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

6 BSA BSA+ Conjugate Molecular Modeling and Docking studies Protein Tertiary Structure Prediction using homology modeling and fold recognition techniques. In silico structure- function studies of proteins and their interactions. Elastase with active site (blue) and docked peptide(yellow)

7 Structure of HLA-B27(Beta2m not shown) Alpha1 & Alpha2 domains in yellow; Alpha3 domain in red; Residues of B27, 169-181 in green Molecular simulations of HLA-B27: Molecular Mechanism for Spondyloarthropathies Simulated Annealing Molecular dynamics under implicit solvent Long Dynamics to explore kinetic stability of Modified Structure Top view Side view

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