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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
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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