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Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering Research in Computational Biology BIC @ IMTECH IT related services (Facilities for IMTECH) Web Servers and Databases 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 Infrastructure for Molecular Modelling IBM Cluster 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 Computer-Aided Drug Discovery Searching Drug Targets: Bioinformatics Comparative genomics Genome Annotation FTGpred: Prediction of Prokaryotic genes EGpred: Prediction of eukaryotic genes GeneBench: Benchmarking of gene finders SRF: Spectral Repeat finder 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 GWFASTA: Genome-Wide FASTA Search GWBLAST: Genome wide BLAST search COPID: Composition based similarity search LGEpred: Gene from protein sequence 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 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 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 TAPpred: for predicting TAP binders Propred1: for promiscuous MHC I binders CTLpred: Prediction of 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 PRRDB: A database of PRRs & ligands Antibp: for anti-bacterial peptides Cytopred: for classification of Cytokines 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. BSA BSA+ Conjugate Elastase with active site (blue) and docked peptide(yellow) Molecular simulations of HLA-B27: Molecular Mechanism for Spondyloarthropathies Top view Side view Structure of HLA-B27(Beta2m not shown) Alpha1 & Alpha2 domains in yellow; Alpha3 domain in red; Residues of B27, 169-181 in green •Simulated Annealing Molecular dynamics under implicit solvent •Long Dynamics to explore kinetic stability of Modified Structure