Bioinformatics Centre Instittute of Microbial Technology, Chandigarh

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Bioinformatics CentreInstittute of Microbial
Technology, Chandigarh
Infrastructure for Protein Modelling and
Engineering
Research in Computational Biology
BIC _at_ IMTECH
IT related services (Facilities for IMTECH)
Web Servers and Databases
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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
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Infrastructure for Molecular Modelling
IBM Cluster

• Hardware
• High Performance Clusters (gt 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 (gt 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

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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
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Modelling of Immune System for Designing
Epitope-based Vaccines
Adaptive Immunity (Cellular Response) Thelper
Epitopes
Propred for promiscuous MHC II
binders MMBpredfor 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
Adaptive Immunity (Cellular Response) 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
Adaptive Immunity (Humoral Response) B-cell
Epitopes
Innate Immunity Pathogen Recognizing Receptors
and ligands
PRRDB A database of PRRs ligands Antibp for
anti-bacterial peptides
Signal transduction in Immune System
Cytopred for classification of Cytokines
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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
BSA
Elastase with active site (blue) and docked
peptide(yellow)
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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