Tips for Research in Bioinformatics

Slides:

Advertisements

Similar presentations

1 Computer-aided Vaccine and Drug Discovery G.P.S. Raghava Understanding immune system Breaking complex problem Adaptive immunity Innate Immunity Vaccine.

Advertisements

1 Support Vector Machine and its Appliactions G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah, India

Introduction and Importance of Bioinformatics: Application in Drug/Vaccine Design G. P. S. Raghava Web:

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Department of Systems Biology Technical University of Denmark Immunological Bioinformatics Introduction to the.

Computer Aided Vaccine Design Dr G P S Raghava. Concept of Drug and Vaccine Concept of Drug Concept of Drug –Kill invaders of foreign pathogens –Inhibit.

The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology.

The Cell, Central Dogma and Human Genome Project.

Host Responses to Viral Infection

Introduction to Bioinformatics Presented By Dr G. P. S. Raghava Co-ordinator, Bioinformatic Centre, IMTECH, Chandigarh, India & Visiting Professor, Pohang.

Epitope Selection Rational Vaccine design. Why? Therapeutic vaccines Therapeutic vaccines Treatment of viral infections (e.g., HIV, HCV), and resistant.

Institute of Microbial Technology, Chandigarh, India

Signaling Pathways and Summary June 30, 2005 Signaling lecture Course summary Tomorrow Next Week Friday, 7/8/05 Morning presentation of writing assignments.

Computer Programs for Biological Problems: Is it Service or Science ? G. P. S. Raghava G. P. S. Raghava G. P. S. Raghava  Simple Computer Programs Immunological.

Immunogen, antigen, epitope, hapten

Computer-Aided Protein Structure Prediction Dr. G.P.S. Raghava, F.N.A. Sc. Bioinformatics Centre Institute of Microbial Technology Institute of Microbial.

Institute of Microbial Technology, Chandigarh, India

Login: BITseminar Pass: BITseminar2011 Login: BITseminar Pass: BITseminar2011.

VACCINOMICS: CURRENT FINDINGS, CHALLENGES AND NOVEL APPROACHES FOR VACCINE DEVELOPMENT Megan Brown Dr. Inna G. Ovsyannikova and Dr. Gregory A. Poland.

Bioinformatics for biomedicine Protein domains and 3D structure Lecture 4, Per Kraulis

My 25 Years in CSIR and in Bioinformatics My 25 Years in CSIR and in Bioinformatics G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah,

In Silico Discovery and Development of BioTherapeutics Background Past decade for extracting knowledge from huge sequence data Major issues addressed:

BIOC3010: Bioinformatics - Revision lecture Dr. Andrew C.R. Martin

Asia’s Largest Global Software & Services Company Genomes to Drugs: A Bioinformatics Perspective Sharmila Mande Bioinformatics Division Advanced Technology.

Methods MHC class-I T cell epitope prediction for Nef Consensus and ancestral sequences of the Nef protein for the different HIV-1 subtypes were obtained.

Problem Statement and Motivation Key Achievements and Future Goals Technical Approach Investigators: Yang Dai Prime Grant Support: NSF High-throughput.

Probe into Discovery and Translational Service in Creative BioMart

Overview of the Immune System Immune System Innate (Nonspecific) Cellular Components Humoral Components Adaptive (Specific) Cell- Mediated Humoral (Ab)

Immune System “Do I still have to go to school doc?”

Secondary Databases Ansuman sahoo Roll: Y Bioinformatics Class Presentation 30 Jan 2013.

Epitope Selection Rational Vaccine design. Immune System Differential distribution of MHC molecules Cell activation affects the level of MHC expression.

CS 790 – Bioinformatics Introduction and overview.

Institute of Microbial Technology, Chandigarh, India

1 Computer-aided Subunit Vaccine Design G.P.S. Raghava, Institute of Microbial Technology, Chandigarh  Understanding immune system  Breaking complex.

Finish up array applications Move on to proteomics Protein microarrays.

1 RNA Bioinformatics Genes and Secondary Structure Anne Haake Rhys Price Jones & Tex Thompson.

1 Computer-aided Drug Discovery G.P.S. Raghava  Annotation of genomes  Searching drug targets  Properties of drug molecules  Protein-chemical interaction.

Web Servers for Predicting Protein Secondary Structure (Regular and Irregular) Dr. G.P.S. Raghava, F.N.A. Sc. Bioinformatics Centre Institute of Microbial.

Telling self from non-self: Learning the language of the Immune System Rose Hoberman and Roni Rosenfeld BioLM Workshop May 2003.

Biological Signal Detection for Protein Function Prediction Investigators: Yang Dai Prime Grant Support: NSF Problem Statement and Motivation Technical.

1 Web Site: Dr. G P S Raghava, Head Bioinformatics Centre Institute of Microbial Technology, Chandigarh, India Prediction.

BioinformaticsDrug InformaticsVaccine Informatics Chemoinformatics

Motif discovery and Protein Databases Tutorial 5.

Central dogma: the story of life RNA DNA Protein.

Bioinformatics Curriculum Issues, goals, curriculum.

Jobs, Careers, Internships, Senior Projects and Research Computer Application Development K-12 education Industrial Training Bioinformatics Validation.

Bioinformatics and Computational Biology

Bioinformatics Lecture to accompany BLAST/ORF finder activity

Proposed Research Problem Solving Environment for T. cruzi Intuitive querying of multiple sets of heterogeneous databases Formulate scientific workflows.

Overview: The Cellular Internet Cell-to-cell communication is essential for multicellular organisms Biologists have discovered some universal mechanisms.

Bioinformatics in Vaccine Design

Major Events in the Local Inflammatory Response.

Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering IT related services (Facilities.

Interferons Induction of synthesis Induction of antiviral activity Antiviral activities induced by interferons  and  Antiviral activities induced by.

Bioinformatics Educated by Zhenglin Zhu School of Life Sciences, Chongqing U.

Randi Vita, M.D. Better living through ontologies at the Immune Epitope Database La Jolla Institute for Allergy & Immunology Division of Vaccine Discovery.

Bioinformatics Overview

Computer-aided Vaccine and Drug Discovery G. P. S

IMMUNOGLOBULIN STRUCTURE AND FUNCTION

Intracellular Pathogens Extracellular Pathogens

7.3 Translation udent_view0/chapter3/animation__how_translation_work s.html.

Molecular Docking Profacgen. The interactions between proteins and other molecules play important roles in various biological processes, including gene.

Ligand Docking to MHC Class I Molecules

Experimental methods in classic epitope discovery

Telling self from non-self: Learning the language of the Immune System

Collaborative RO1 with NCBO

BSC1010: Intro to Biology I K. Maltz Chapter 21.

Computer-Aided Protein Structure Prediction

Computer-Aided Protein Structure Prediction

Evolution of Genomes Chapter 21.

Computer-Aided Protein Structure Prediction

Presentation transcript:

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

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?)

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

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

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)

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

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

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

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

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

Multiple layers of the immune system

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

Components vs System Biology

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

Role of Bioinformatics in Designing Theraputic Peptides

Important Information in Manual for Develpers Thankyou

Thankyou

Thankyou

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

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

Thank You Important URLs http://www.imtech.res.in/raghava/ http://www.imtech.res.in/raghava/gpsr/ http://www.imtech.res.in/raghava/reprints/ http://www.imtech.res.in/raghava/slides/ http://crdd.osdd.net/ http://crdd.osdd.net/raghava/ccpdb/