Bioinformatics Centre Instittute of Microbial Technology Chandigarh Infrastructure

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Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering Research

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

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 in 1998 Computing Ab/Ag concentration from ELISA data

Infrastructure for Molecular Modelling IBM Cluster Hardware • High Performance Clusters (> 10 Teraflops)

Infrastructure for Molecular Modelling IBM Cluster Hardware • High Performance Clusters (> 10 Teraflops) – IBM 14 node, 28 core, P 6 processos (Best for protein modelling) – SUN HPC/Webserver (160 core AMD), Best for webservices – Supercomputer 400 core of Xeon 3. 2 GHz (> 6 Teraflops) • Bioinformatics cluster: 4 node Apple G 5 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

Computer-Aided Drug Discovery Searching Drug Targets: Bioinformatics Comparative genomics Genome Annotation FTGpred: Prediction of Prokaryotic genes EGpred: Prediction of eukaryotic genes Gene. Bench: 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 APSSP 2: protein secondary structure prediction Betatpred: Consensus method for -turns prediction Bteval: Benchmarking of -turns prediction Beta. Turns: Prediction of -turn types in proteins Turn Predictions: Prediction of / / -turns in proteins Gamma. Pred: Prediction of-turns in proteins Bhair. Pred: Prediction of Beta Hairpins TBBpred: Prediction of trans membrane beta barrel proteins SARpred: Prediction of surface accessibility (real accessibility) Pep. Str: Prediction of tertiary structure of Bioactive peptides

Modelling of Immune System for Designing Epitope-based Vaccines Adaptive Immunity (Cellular Response) : Thelper

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 MHC 2 pred: 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 Propred 1: 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 Ig. E eptopes Hapten. DB: 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

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+ Conjugate Elastase with active site (blue) and docked peptide(yellow)

Molecular simulations of HLA-B 27: Molecular Mechanism for Spondyloarthropathies Top view Side view Structure

Molecular simulations of HLA-B 27: Molecular Mechanism for Spondyloarthropathies Top view Side view Structure of HLA-B 27(Beta 2 m not shown) Alpha 1 & Alpha 2 domains in yellow; Alpha 3 domain in red; Residues of B 27, 169 -181 in green • Simulated Annealing Molecular dynamics under implicit solvent • Long Dynamics to explore kinetic stability of Modified Structure