1. INTRODUCTION TO BIOINFORMATICS Department of Pharmaceutics, School of Pharmacy, Bharat Institute of Technology, By-Pass road, Paratapur, MeerutSUBMITTED TO- MS. NEHA GULATI SUBMITTED BY – PROMILA SHARANASISTANT PROF. PHARMACEUTICS M.PHARMA 1 ST SEM
2. CONTENTS INTODUCTION TO BIOINFORMATICS. EMERGENCE OF BIOINFORMATICS . AIM OF BIOINFORMATICS. APPLICATION OF BIOINFORMATICS. TOOLS AND TECHNIQUES.o IN DRUG DESIGNo RATIONAL DRUG DELIVERY. BIOINFORMATICS CENTERS IN INDIA. DATABASEo APPLICATIONSo CLASSIFICATION
3. INTRODUCTION TO BIOINFORMATICSIt is a branch of science that deals with the study of biological information by using computer technology.Computers are used to gather , store , analyze ,and integrate the biological information which can then beapplied to the gene based drugs discoveries and development.Bioinformatics –(Molecular) bio – informatics: bioinformatics is conceptualizing biology interms of molecules (in the sense of Physical chemistry) and applying “informaticstechniques” (derived from disciplines such as applied maths, computerscience and statistics) to understand and organize the information associatedwith these molecules, on a large scale. In short, bioinformatics is a managementinformation system for molecular biology and has many practical applications.As submitted to the Oxford English Dictionary.
4. The Emergence Of Bioinformatics.Bioinformatics is a sub-field of the Biological SciencesBioinformatics is highly interdisciplinary and draws upon the following areas of study to solve biologicalproblems:• Applied Mathematics• Statistics• Computer Science• Also referred to as Computational BiologyThe Emergence Of Bioinformatics• With the discovery of DNA came a desire among biologists to understand how genetic structure affects the biological traits of organisms• Sequencing is not sufficient (95% of human genome is “junk” DNA)• Genes must be identified and correlated with the functions of their corresponding proteins• Biological phenomena must then be linked to protein identity, structure, and genomic originAs a result, powerful new data management and analysis methods were developed – These methods were precursors to current research in bioinformatics – Recent progress in several sub-fields of biology is resulting in a boom in database size and complexity – Consequently, there is a great need in many areas of biology for efficient database management and new computer- based analytical techniques
5. GOAL: To increasing the understanding of various biological techniques /processes like :• Mapping of DNA• Analyzing DNA• To study /view / create 3D models of protein structures is being done.• To organize data in a way that allows researchers to access existing information and to submit new entries as they are produced, e.g. the Protein Data Bank for 3D macromolecular structures APPPOACHES OF BOINFORMATICS. STATIC DYANAMICSequence Structure Interaction Reaction Multi agent Variable concentration Data Fluxes based modeling of metabolite• To develop tool sand resources that aid in the analysis of data. For example, having sequenced a particular protein, it is of interest to compare it with previously characterized sequences
6. APPLICATIONS OF BIOINFORMATICSBioinformatics is applicable in various fields including: More target drugs Personalized medicines Preventive medicines Gene therapyMicrobial genomic applications: Biotechnology Antibiotic resistance Forensic analysis of microbes Bio weapons creationsAgriculture : Crops management. Improvement in nutritional qualities
7.  Sequence analysis Genome annotation Computational evolutionary biology Analysis of gene expression Analysis of mutation in cancer Comparative genomics Modeling biological system Prediction of protein structures Drug design discoveryCOMMONLY USED SOFTWARE TOOLS /TECHNIQUES ARE: -In production and display of protein structure. -Nucleic Acid Modeling Tool :Structure modification of single or double stranded DNA or RNA . Identification of protein functions. -Prediction of protein structures. – Editing manipulation and analysis of Nucleic Acid and protein sequence . - Analysis of protein structures. - Structures and functions of genes and proteins.
8. Drug Design Software and Tools:1.Sanjeevini A complete drug design software.2. Binding Affinity Prediction of Protein-Ligand Server(BAPPL) Computes the binding free energy of a protein-ligand complex.3. Binding Affinity Prediction of Protein-Ligand complex containing Zinc Server(BAPPL-Z)Computes the binding free energy of a metalloprotein-ligand complex containing zinc.4. Drug-DNA Interaction Energy (PreDDICTA) Calculates the Drug-DNA interaction energy.5. ParDOCK - Automated Server for Rigid Docking Predicts the binding mode of the ligand in receptor target site.6. Active Site Prediction
9. How scientists can use bioinformatics to aid Rational Drug Discovery.
10. Sequence analysis:DNA sequence of organisms are decoded & stored in databases. This sequence information is then analyzed todetermine that encoded protein. B.L.A.S.T. is used to search DNA sequence in the drugs.Computational Evolutionary Biology:Here the study of origin of species well as the changes they acquire over a large periods can be measured bytracing the changes in their respective DNA rather studying there physical taxonomy or physiological changes.Analysis of protein expression :HTMS (High Through Mass Spectrometry) can provide a snapshot of the proteins present in biological samplesPeptool – used for identification of protein formations.Analysis of Mutation in Cancer:In cancer the genomes of affected cells are rearranged in complex ways , so various techniques are used toidentify unknown mutations in variety of genes in cancer- Oligonucleotides micro arrays – to identify the chromosomal gains & losses. Single nucleotides polymorphism arrays-- to detect mutations.Image analysis :Computational techniques are used for biomedical imagining is very important for both diagnostic & research:
11. BIOINFORMATICS CENTERS IN INDIA1). Indian Institute of Technology, Hauz Khas, New Delhi.2). Rice Genome Initiative Department of Plant Molecular Biology, South Campus B.J. Road, University of Delhi.3). School of Biological Sciences, Madurai Kamraj University, Madurai.4). Department of Physics, Indian Institute of Science Malleswaram, Bangalore.5). National Institute of Immunology, Shahid Jeet Singh Marg JNU.6). Institute of Microbial Technology, Sector 39A Chandigarh.7). Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi.8). Bioinformatics Centre University of Pune, Ganeshkhind Pune.9). Institute of Genomics & Integrative Biology, Delhi University Campus, Mall Road near Jubilee Hall Delhi.10). National Brain Research Centre, Gurgaon, Haryana.11). Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad.12). JNU Bioinformatics Center, JNU New Mehrauli Road.
12. WHAT IS A DATABASE?Data and databases are key to both bioinformatics and cheminformatics. Without large quantities of easilyaccessible electronic data, most kinds of data searches would prove to be fruitless , and most kinds ofpredictive or analytical software could never be developed or tested.Application of Data Base Management in Pharmacy 24x7 best efforts support & basic database maintenance and patching Perform daily export backup & operational monitoring Setup a database account Setup database& setup monitoring Single instance database (Oracle, SQL, Mysql) User does schema, tables, views and procedures User has full responsibility to run the database Assist with minor Data Migrations / Updates Assist with releases twice per quarter Assist with testing of scripts Migration from test to production
13. Major freely available Public Domaindatabases & data Bioinformatics mining tools Facilities National enter Of Biotechnology European Genome NET information Bioinformatics (KEGG & DDBI) (NCBI)United Institutes (EBI) Japan states Database Analysis tools BLASTA-sequence Recognition tools for Sequence alignment searching sequence & structures tools
14. CONCLUSIONBioinformatics have stretched its wings over the end less boundaries ofspectacular success , world wide recognition and remote communication atevery nook and corner in this world. There are certain sectors wherebiotechnology is playing its vital role which we have previously discussed.The advancements in the field of Bioinformatics are leading to morefocused area of study at Systems level. Taking note of this trend the centerhas renamed it as “Centre for Computational Biology and Bioinformatics(CCBB)”. The main objective should be of human resource developmentactivities and research in frontier areas of computational biology has taken ashape and recognition within the country. We are also making back breakingeffort in inter–institutional collaboration in research projects. To keeprhythm with the development in the field, importance is given to set up thenecessary infrastructure and resources for the academic community.
15. REFERENCE:• N. M. Luscombe, D. Greenbaum, M. Gerstein,Department of Molecular Biophysics and Biochemistry Yale University, New Haven, USA.• Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi.• http://www.soe.ucsc.edu/programs/bioinformatics/graduate/.• Kok K, Naylor SL, Buys CH. Deletions of the short arm of chromosome 3 in solid tumors and the search for suppressor genes.Advances in Cancer Research 1997; 71: 27-92.• Syngal S, et al. Sensitivity and specificity of clinical criteria for hereditary non- polyposis colorectal cancer associated mutations in MSH2 and MLH1. Journal Med Genet 2000; 37 (9): 641-5.