1. Tips for Research in Bioinformatics
Scope and Importance of Bioinformatics
Do you have required skill?
Type of bioinformaticians (Users, Analysis or Developer)
Possible biological problems
Protein/Peptide related bioinformatics
Types of methods and use of Open Source
How to start
Linux, programming (PHP/perl)
WAMP/LAMP (Linux/Windows, Apache, Mysql, PHP)
Machine learning techniques (Weka)
Beware with experimental biologist

2. Concept of Research in Bioinformatics
Bioinformatics vs Computational Biology
Service vs Research
Components vs System Biology
Guidelines/Suggestions
Role of technical expertise
Our group (Service or Science?)

3. Bioinformatics Vs Computational Biology
Computational Biology Examples
Ramachandran Plot
Proteins Structure Prediction (Ab-initio)
Dynamic Programming for Alignment
Examples of Bioinformatics
BLAST search against sequence databases
Homology Modelling
Epitope Mapping

4. Service Vs Bioinformatics Research
BTIS Programme
NCBI and EBI Services
Web service / databases
New rules or models derived from known structures
New functional domain form experimental data
Discoveries based on data
Service for better research
Research for better service
Range of service (Individual or Community)
Collaboration with experimental scientist for validation

5. Suggestions Selection of Problem
Talk to biologist & understand their problem
Raise question in your mind
Read literature (self learning) for answer
Raise more question and read again
Work on important problem
Select problem if large dataset is availble
Develop method with high accuracy
Validate using standard validation techniques
Develop web server software for service
Publish in appropriate journal (high IF)

6. Fingerprinting Technique
Microarray Data
Fingerprinting Technique
Subcellular Localization
Fingerprinting Technique
Whole genome Sequencing
Assembling of Genomes
Genome Annotation
Epitope based Vaccines
Anotation of Proteomes
Drug Discover
Drug targets
Comparative Genomics
Development of Databses
RNA Interference

7. Therapeutic Application of Proteins/Peptides
Peptide based Drugs (Small Molecule, Peptide, Protein)
Anticancer peptides
Antibacterial peptides
Peptide for delivering drug
Cell-penetrating peptides
Tumor-homing peptides
Peptide as disease diagnostics
Disease specific Mimotopes
Epitope/Peptide based Vaccines
T-cell epitopes
B-cell epitopes

8. Limitation of Peptides & Challenges for Bioinformaticians
Peptide Degradation (short half-life)
Large peptide degrading enzymes
Hepatic/renal Clearance (liver/kidenys)
Low Oral Bioavailability (injection)
High conformational flexibility
Environment dependent tertiary structure
Low selectivity
Immunogenicity and antigenicity
High cost of production & Storage
Modification/glycosylation of peptides

9. Drug/inhibitor/vaccine/ Disease Diagnostics
Peptide-Protein Interaction
Peptide Structure, docked structure
Adaptive Immunity: B-cell, T-cell Epitope
Innate Immunity: Toll-like receptors
Anti-(bacterial , microbial, cancer, viral) peptides
Mimotopes for diseases diagnostics
Structure determination: Natural, non-natural , modified bonds
Structure prediction: Natural, non-natural , modified bonds
Peptide or Protein
Synthesis: Phase display, SPSS, Codon Suffeling
Natural bioactive peptides from metagenomics
Mimotopes for B/T epitopes
Mimicking of Drug Molecules
ADMET: Proteolytic enzymes, Half-life
Size Optimization for function/Str.
Oral Delivery : Trans. & Adjuvant

10. Epitopes (Subunit Vaccine)
Innate Immunity
Vaccine Delivery
Protective Antigens
Adaptive Immunity
Vaccine Informatics
Bioinformatics Centre
IMTECH, Chandigarh
WHOLE
ORGANISM
Attenuated
Epitopes (Subunit Vaccine)
Purified Antigen
T cell epitope

11. Multiple layers of the immune system

12. Disease Causing Agents
Innate Immunity
Vaccine Delivery
Protective Antigens
Adaptive Immunity
Vaccine Informatics
Bioinformatics Centre
IMTECH, Chandigarh
Disease Causing Agents
Pathogens/Invaders

13. Components vs System Biology

14. Innate Immunity : Pathogen Recognizing Receptors and ligands
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
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

15. Role of Bioinformatics in Designing Theraputic Peptides

16. Important Information in Manual for Develpers
Thankyou

17. Thankyou

18. Thankyou

22. 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

23. Suggestions Technical Learning
Linux/Unix system
Programming language PERL/PHP/C
Example Scripts ( )
HTML and CGI script (Java)
LAMP learning
SVM_Light for SVM, SNNNS for ANN
TREMBL for nearest neighbour
Weka for wide range
Rapidminer

24. Thank You Important URLs http://www.imtech.res.in/raghava/