STRUCTURAL ELUCIDATION AND INTERACTION AMONG
BIOLOGICAL MOLECULES
Unit I
Fundamentals of chemical bonding and non-bonding interactions: Electrovalent bond, stability of electrovalent bond, stability of electrovalent compounds; Co-valent bond-shape of orbitals and hybridization. Molecular geometry, partial ionic character of covalent bonds. Co-ordination bond, Vander Waals forces; Metallic bond.
Unit II
Fundamentals of atomic and molecular orbitals: Theory of atomic and molecular Orbitals: Linear combination of atomic orbitals; Quantitative treatment of valency bond theory and molecular orbital theory; Resonance structures; a- bonds and 1- bonds.
Unit III
X-Ray crystallography of biomolecules; Generation of X-rays and its characteristic properties; X-ray diffraction; Bragg's law-unit cell and lattice of crystals; X-ray crystals of proteins and nucleic acids.
Unit IV
Spectroscopy: Spectroscopy of molecules: UV,IR, NMR, (elementary treatment).
Unit V
Fundamentals of stereochemistry: Theory of co-valent bonds; Directional properties of covalent bonds; Stereochemistry of proteins and nucleic acids.
Reference Books
1.
Albert cotton, F. 1997, Chemical Applications of Group Theory, John Wiley and Sons Inc., New York.
2.
Ernest Eliel 1996, Stereochemistry of carbon compounds, Prentice Hall.
3.
Spice, J. E. 1994, Chemical Bonding and Structure, Pergamom Press Ltd., Headington Hill Hall, Oxford.
4.
Winter, M. J. 1996, Oxford University Press Inc., New York
CHEMISTRY OF BIOMOLECULES AND THEIR DYNAMICS
Unit I
Chemical foundations of biology- pH, pK, acids, bases, ouffers, weak bonds, covalent bonds. Principles of .hermodynamics. Classes of organic acids and their unctional groups- atomic and molecular dimensions, space illing& ball& stick model. Amino acids and peptides-31assification, (Chemical reactions and physical properties, sugars classifications and reactions.
Unit II
Heterocyclic compounds and secondary metabolites in living system nucleotides, pigments, isoprenoids. Separation techniques of different biomolecules. Lipid -Classification, Structure and functions. Proteins and Nucleic acids, Classification, separation; purification and ciriteria of homogeneity, end group analysis, hierarchy in structure.
Unit III
Polysaccharides-types, structural features, methods for compositional analysis, Analytical techniques in biochemistry and biophysics for small molecules and macromolecules for quantitation.
Unit IV
Potential energy calculations using semiemperical and quantum chemicals, potential energy function. Electrostatic energy surface generation. Methods to predict secondary structures of polymers. Methods to predict three dimensional structure of proteins, nucleic acids- rRNA and DNA using dynamic programming methods.
Unit V
Molecular mechanism and Molecular dynamics Oligopeptides, Nucleotides, Proteins, Drug Molecules Pesticides. Docking of molecules, knowledge-based structure prediction, Molecular design, Emerging areas in bioinformatics, biocomputing.
Reference Books
1.
Baxevanis A., Ouellette F. B. F (Eds) 1998, Bioinformatics: a practical guide to the analysis of genes and proteins, John Wiley and Sons, New York.
2.
Charles, R., Cautor and Paul, R., Schinmmel, W.H. 1980, Biophysical chemistry Part I, II, III, Freeman company . San Francis Co., U. S.
3.
Lesk, A. M., 1988, Computational Molecular Biology. Sources and methods for sequence analysis, Oxford ( University Press, Oxford.
Wilkins, M. R., Williams, K. L., Appel, R. D.,Hochstrassser, D. H., (Eds) 1997, Proteome research; a new frontiers in functional genomics, Stringer Verlag, Berlin.
CELL BIOLOGY
Unit I
Cell theory - Prokaryotic and eukaryotic cells - Animal and plant cell. Molecular models of cell wall and cell membrane- Structure and function.
Unit II
Ultra structure and function of all Cell organelles Mitochondrial and Chloroplast genomes. Gene transfer techniques: Vector and Vectorless modes of gene transfer plastome transformation. Gene targeting (Ti plasmid, Baculovirus, Adenovirus, SV40, M13 etc)
Unit III
Chromosomal architecture, Classification, its aberrations and banding techniques. Replication, transcription, translation, Protein sorting and targeting chaperones.
Unit IV
Regulation of gene expression in prokaryotes and Eukaryotes, transposons and genetic recombination.
Unit V
Cell Cycle- Mitosis, Meiosis - Tools to study cell biology- PCR types and their applications. Cell- cell adhesion and communication, Cell-Matrix adhesion, Collagen and Non-collagen components of Extracellular Matrix. Cell death and its regulation.
Reference Books
1.
Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter. 2002, Molecular Biology of the Cell. 4th ed. Garland Publishing., New York.
2.
Benjamin Lewin, 2002, Gene VII, Oxford University Press, Oxford.
3.
Cooper, Geoffrey M, 2000, The Cell - A Molecular Approach. 2nd ed Sinauer Associates, Inc; Sunderland (MA)
4.
De Robertis, E. D. P., De Robertis, E. M. F., 2001, Cell and Molecular Biology, Ethan Bier, 1990, The Coiled Spring, Cold Spring Harbor Press.
5.
Freedman, L. P., Birkhuser, 1994, Molecular Biology of Steroid and Nuclear Hormone receptors.
6.
Gilbert, S. F., 1990, Developmental Biology, Sinauer Associates Inc. Lippincott Williams and Wilkins, New York.
7.
Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E, 2000, Molecular cell biology 4th edition. W.H.Freeman & Co., New York.
8.
Longo, F. T., 1993, Fertilization, Chapman and Hall.
9.
Wilson, E. B., 1993, Cell in development and Inheritance, MacMillan, New York.
10.
Watson, T. J., 1987, The Molecular Biology of the Gene, Benjamin Cummings.
RELATIONAL DATABASE MANAGEMENT SYSTEMS
Unit I
Introduction: Purpose of database systems- overall system structure - Entity relationship model: Entities and Entity sets, relationships- mapping constraints- primary keys- ER diagram.
Relational database: SQL, basic structure, set operations, aggregate functions, nested subqueries, Views, Complex Queries, Modification of the database, Joined relations, data definition language, Embedded SQL, Dynamic SQL.
Unit IV
Relational database design: pitfalls - Normalization using functional dependencies- Decomposition - Boyce Codd Normal Form- Third normal form - Normalization using multi valued dependencies- Fourth Normal form-Normalization using join dependencies- Domain key Normal form. Network data model and Hierarchical data model.
Unit V
Query processing, query optimization, Concurrency control, database security and integrity- distributed database. Case study of typical system - Oracle.
Reference Books
1.
Hector Garcia-Molina, Jeffrey D. Ullman, Jennifer D Widom, 2002, Database systems, the complete book. Prentice Hall
2.
"Henry F. Korth and Abraham Silberschatz, 2000. Database systems concepts, McGraw Hill International Publication
3.
Jeffrey, D. Ulman, 1998, Principles of database systems, Galgotia Publishers
4.
Kifer, Michael, Bernstein, Arthur, Lewis, Philip M 2000, Database Systems: An Application Oriented Approach Complete. Addison - Wesley publications.
5.
Sdate, C. J., 1995, An Introduction to database systems, 3rd Edition, Narosa.
Practical I - Cell Biology
1.
Staining techniques
2.
Stains and staining procedures
3.
Instrumental Methods for cell biology.
4.
Microtomy
5.
Histochemical techniques
6.
Mitosis and Meiosis
7.
Cell fractionation Methods.
Practical II- Relational database management systems
1.
ORACLE
Table creation- simple queries, Report creation using column format, Built in functions of SQL, PL/SQL- Student information processing, write a database trigger to implement the concept of master-detail relationship, using P1/SQL prepare electricity bill.
2.
DEVELOPER 2000
Use forms and menu to prepare payroll system and when the form is executed the window should be in maximized state, use forms to prepare income tax report (with using SQL *Report writer), create a form for seat reservation problem of road transport (without using SQL*Report writer), Create a report using tables order and item: such that there is a break in every order and print group wise total and grand total, Create report using tables using order and item. Print the group wise total and grand total. The style of reports should be master detail.
3.
Prediction of protein secondary structure using dynamic programming
4.
Prediction of 3D structure of proteins using dynamic programming
5.
Prediction of 3D structure of DNA using dynamic programming
6.
Prediction of 3D structure of t-RNA using dynamic programming
7.
Amino acid composition and Molecular Weight of a protein determination.
8.
Motif and Domain of protein- identification.
9.
Signal peptide determination
SEMESTER II
PARALLEL COMPUTING AND PROGRAMMING IN PERL
Unit I
Trends towards parallel computing - Flynn's architectural classification scheme - Parallel processing applications. Principles of linear pipelining classification of pipeline computers- Design of pipeline processors interleaved memory organization - Vectorization techniques vectorizing compiler.
Unit II
Multi processor system- classification and organization interconnection networks - classification of multiprocessor operating systems- Task scheduling and load balancing parallelization techniques. Case study: ILLIAC -IV. Static data flow computers - statolic architectures- SIMO algorithms- Matrix transposition on shared multiplication on shared memory system - Mesh connected system and cube connected system. Case study: Cray X- µp. MIMD Algorithms - Solving systems of linear equations finding roots of nonlinear equations. MIMD enumeration sort.
Unit III
Introduction to C: Constants, variables and datatypes operators and expression, managing input and output operators, decision making and looping, arrays
Programming in C++: Handling of character strings, user defined functions, structures and unions, pointers, file management in C, dynamic memory, allocation and linked
lists.
Unit IV
Web programming with PERL script- PERL Standard library- Sequence analysis with web based Object oriented programming in PERL - Advanced data manipulation -Database programming with PERL. PERL CGI Programming-Internet - Related Library, Modules and utilities for PERL tools, Building phylogenetic trees.
Unit V
Advanced searching - PSI- BLAST and PHI- BLAST-gene Prediction programs. Writing PERL for sequence analysis - Building PERL script from search - Automate sequence analysis - Bioinformatics for drug discovery.
Reference Books
1.
1Akil, S. G., 1999, The Design and analysis of parallel Algorithms, PHI
2.
Andreas, D., Baxevanis, B. F., Francis Ouellette, 2001, bioinformatics- A practical guide to the analysis of Genes and Proteins, Wiley Inter Science.
3.
Bhatkar, Basu, Purchi and rege, 1998, Forntierin parallel computing, MGH
4.
Birren, B.E., Green P.Hieter, Klapholz, S., 200, Gemone Analysis Laboratory Manual, vol 1 to 4, Cold Spring Harbor Laboratory press.
5.
Fountain, T.J., Shute, M.J.,1990, Multiprocessor Computer and Architecture, Borth Holland.
6.
Hwang, K., Driggs, f.A., 1994, Computer Architecture and parallel processing, MGH
7.
James Tisdall, 2001, Beginning Perl for Bioinformatics O' REILLY.
8.
Micheal Mc Millan, 1998, PERL from the ground up covers PERL for UNIX, Windows 95 and Windows NT environment, TMGH.
9.
Paul Du Bois, 2002, Mysql and Perl for the Web, SAMS Publishing
10.
Peter Wain Wright, SPD, 2001, Professional PERL Programming ( WROX series)
11.
Quinn, M.J., 1995, Desisning Efficient Algorithms for parallel Computer, Narosa.
12.
Randal L.Schwartz, Tom Phoenix, 2001, Learning Perl, 3rd Edition O' REILLY.
13.
Shishir gundavaram, Scott Guelich, Gunther Birznieks, 2000, CGI Programming with Perl, 2nd Edition O' REILLY.
MOLECULAR BIOLOGY
Unit I
Introduction to molecular biology and genetics - DNA replication; Prokaryotic and eukaryotic DNA replication - Enzymes and Accessory proteins involved in DNA replication -
DNA damage, repair and recombination.
Unit II
Prokaryotic transcription- Eukaryotic transcription- RNA polymerase- General & specific transcription factors- regulatory elements and mechanisms of transcription regulation. Modifications in RNA: 5' - cap formation- transcription- termination- 3'-end processing and polyadenylation- splicing - editing, nuclear export of rnRNA, rnRNA stability.
Unit III
Translation: Prokaryotic translation- Eukaryotic translation- Mechanism of initiation, elongation and termination- Regulation of translation - Co- and post -translational modifications of proteins - synthesis of secretory and membrane proteins - Import into nucleus, mitochondria, Chloroplast and peroxisomes, Receptor mediated endocytosis. Lac Operon, Tryptophan Operon.
Unit IV
Biology of plasmids - discovery, types and structure of F, RTF, Col- factors and Ti. Replication and partitioning Incompatibility and copy number control. Natural and artificial plasmid transfer and their applications.
Transposable genetic elements- Oncogenes and tumour suppressor genes- viral and cellular oncogenes - Tumor suppressor genes from humans, structure, function and mechanism of RB and p53 tumor suppressor proteins.
Unit V
Molecular mapping of genome: Genetic and physical maps - physical mapping and map based cloning- choice of mapping population - simple sequence repeat loci- southern and flouresence insitu hybridization for genome analysis- chromosome micro dissection and micro cloning- Molecular markers in genome analysis. RFLP, RAPD and AFLP analysis- application of RFLP in forensic, disease prognosis genetic counseling, taxonomy and biodiversity etc.,
Reference Books
1.
Alberts, Bruce; Johnson, Alexander; Lewis, Julian: Raff, Martin; Roberts, Keith; Walter, Peter. 2002, Molecular Biology of the Cell. 4th ed. Garland Publishing., New York
Dabre, P. D., 1998, Introduction to Practical Molecular Biology, John Wiley and Sons Ltd., New York.
4.
Dale, J. W., 1994, Molecular Genetics of the Bacteria, John Wiley and Sons.
5.
Keith Wilson, John Walker, 2005, Principles And Techniques of Biochemistry And Molecular Biology .
6.
Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E, 2000, Molecular cell biology 4th edition. W.H.Freeman & Co., New York.
7.
Sambrook, J., Fritsch, E. F., Maniatis, T., 2000, Molecular Cloning: A laboratory manual, Cold Spring Harbor Laboratory Press, New York.
8.
Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz,J. A., Weiner, A. M., 1987,
9.
Molecular Biology of the Gene,(4th edition), The Benjamin Cummings Publication Co. Inc.,California.
GENETIC ENGINEERING
Unit I
Enzymes In Genetic Engineering - Restriction Endonucleases - Ligases - Alkaline Phosophatase - Polynucleotide kinase - Terminal Deoxynucleotidyl III transferase- S1 Nuclease DNA PolymeraseI Holo Enzyme DNA Polymerase III, Klenow Fragment - TAQ DNA Polymerase - RNases - Ribonuclease - Reverse Transcriptase- Poly (A) Polymerase - Deoxyribonuclease.
Unit II
VECTORS - Plasmids - Replication - Size - Copy number - Amplification - Types PUC plasmids - Isolation Plasmid DNA - criteria for Plasmid cloning; Cloning vectors based on Bacterial Plasmids - Plasmid pBR322 - origin- advantage - Col El Plasmid DNA - Col El Amp Plasmid DNA - pBR325 Plasmid DNA - pMB9 Plasmid DNA - pTZ Plasmids, Bacteriophage Vector for E coli - Phage as a vector-Lambda replacement and insertion vectors - M13
Bacteriophage Baculovirus- Genetic organization construction; Cosmid vectors and their use, Virus vector for animalcells, Vector for plant cells ;Shuttle vector Expression Vectors.
Unit III
Core techniques is gene manipulating; Cutting and joining DNA, Introduction of DNA into cells, Cloning Strategies, construction of genomic libraries and cDNA Libraries - Probe construction, labeling.
Unit IV
Methods of selection and screening of recombinant DNA - Gene transfer techniques. Molecular mechanism of Antisense Technology, Inhibition of splicing, Poly Adenylation & translation, Distruption of RNA structure & Capping - Application of Antisensing Technology.
Unit V
Genetic Engineering Technique and Applications RAPD, RFLP, Micro array & sequencing and PCR and their applications, safety regulations in recombinant DNA, Terminator gene technology, Ethics.
Reference
1.
Glover, D. M., Hames, B. D., 1995, DNA CLoning I and II, IRL Press.
2.
Innis, M. A., Gelfant, D. H., Sninskey, J. J., 1995, PCR Strategies, IRL Press
3.
Murray, E.T., 1991, Gene Transfer and Expression protocols-methods in molecular biology, vol 7, Humana Press.
Puhler, A., 1993, Genetic Engineering of Animals,VCH Publishers, Weninheim FRG.
6.
T A Brown, 2001, Essential Molecular Biology: Volume Two, a practical Approach, Oxford university press.
7.
T A Brown, 2001, Gene cloning AND Analysis: An Introduction , Blackwell Publications
8.
Watson, J.W., Gillman, M., Witknow Ski, M., Zoller,M., 1992, Recombinant DNA ( 2nd Edition ), , Scientific Americans Books, New York.
PROTEOMICS AND GENOMICS
Unit I
Overview of sequence analysis: Database, data mining, Algorithms in proteomics, Applications of proteomics: Proteome mining, protein expression profiling, protein-protein interactions, protein modifications; automation
Unit II
2D Electrophoresis, IEF, HPLC, Protein digestion techniques; Mass Spectrophotometry: MALDI-TOF, Mass analyzers, peptide Mass Finger printing; Protein arrays.
Unit III
Overview of genome; genome sequence acquistion and analysis; comparitive homologies, evolutionary changes; SNPs; Genetic analysis; Linkage mapping and analysis; High resolution chromosome maps; Physical mapping, YAC, Hybrid mapping, strategies, microarrays; sequence specific tags (SST), Sequence - tagged sites (STS), ISH, FISH, RFLP, RAPD.
Unit IV
Variations in sequencing methods; Ladder, fluorescent, Mass spectrometry, shot gun, transport -Mediated, autimated sequencing; Finding gene mutations; implications of DNA sequencing; implications of sequencing genomes.
Unit V
Construction and screening of cDNA libraries; PCR Variations in PCR: cDNA microarrays, gene disruptions, Yeast two-hybrid system, Serial analysis of gene expression (SAGE), SAGE adaptation for downsized extracts (SADE); applications of DNA arrays, Pharmacogenomics.
References
1.
Glover, D. M., Hames, B. D., 1995, DNA CLonong I and II, IRL Press.
2.
Innis, M. A., Gelfant, D. H., Sninskey, J. J., 1995, PCR Strategies, IRL Press
3.
Murray, E. T., 1991, Gene Transfer and Expression protocols-methods in molecular biology, vol 7, Humana Press
4.
Old, R. N., Primrose, S. B., 1994, Principles of gene manipulations, Blackwell Scientific Publications.
6.
Puhler, A., 1993, Genetic Engineering of Animals, VCH Publishers, Weninheim FRG.
7.
T A Brown, 2001, Essential Molecular Biology: Volume Two, a Practical Approach, Oxford university press.
8.
T A Brown, 2001, Gene Cloning and DNA Analysis: An Introduction, Blackwell Publications.
9.
Watson, J. W., Gillman, M., Witknow Ski, M., Zoller, M., 1992, Recombinant DNA(2nd Edition), Scientific Americans Books, New York.
10.
Bioinformatics sequence and genome analysis. Mount, David W. Cold Spring Harbor Laboratories press, CSH New York, 2001
11.
Introduction to proteomics. Tools for the new biology. Liebler, Humana Press 1st Ed. December, 2001
12.
Proteomics: From protein sequence to function S. Pennington, M. J. Dunn Bios Scientific Publications Ltd. 2nd Ed. (Jan 15,2001)
Practical III- Parallel computing and programming in PERL
PERL Programming to convert
a. the DNA sequence into mRNA.
b. the mRNA sequence into cDNA.
c. the mRNA into aminoacid sequence.
PERL programming to findout
a. the translated product of the given DNA sequence.
b. the restriction sites in a DNA sequence.
c. the promoter site in a particular DNA sequence.
d. the Exon and Intron region within the gene sequence
Practical IV - Molecular biology and Genetic Engineering
Single cell colony isolation - checking for genetic markers.
Isolation of antibiotic resistant and autographic mutants.
Salivary gland chromosome-Chironomos.
UV Survival Curve.
Isolation of DNA.
Isolation of Plasmid
Extraction of total DNA from Plant/Animal Tissue (Agarose gel electrophoresis)
Restriction digestion
Blotting techniques (Demonstration)
PCR amplification
DNA - Sequencing demonstration
Estimation of Nucleic Acids (DNA 8b RNA)
Ligation (Kit)
RFLP
Protein characterization by coomasie blue & silver staining.
SEMESTER III
BIOLOGICAL DATABANKS AND ANALYSIS
Unit I
Data ware housing, data capture, data analysis, Sequence data banks, Introduction to Sequence data bank - Protein sequence data banks NBRF-PIR, SWISSPR0T, signal peptide databank. Nucleic acid sequence data bank, Genbank, EMBL, Nucleotide sequence data bank. AIDS virus sequence data bank, tRNA data bank.
Unit II
Analysis tools for sequence data banks. Pair wise alignment-NEEDLEMAN and Wunch algorithm; Smith Waterman algorithm. Multiple alignment - CLUSTAL, PRAS.
Unit III
BLAST & FASTA types and their algorithms, Structural data banks - Protein DataBank (PDB), The Cambridge Structural Database(CSD), Genome data bank, Metabolic pathway data, Composite protein sequence databases.
Unit IV
Protein classification, secondary and tertiary structure prediction, GOR Method, Chou-Fasman method, HMMs, Neural networks, Blocks and Profile analysis. Phylogenetic analysis- Maximum parsimony, Maximum Likelihood, UPGMA methods.
Unit V
Microbial and cellular data banks, Introduction to MSDN (Microbial Strain Data Network), Numerical coding systems of microbes, Hybridoma data bank structure, Virus information system, cell line information system, Other important data banks in the area of Biotechnology / Life sciences / Biodiversity.
References
1.
Adams, M. D., Fields, C, Venter, J. C, 1994, Automated DNA sequencing and Analysis, Academic Press, London.
2.
Bishop, M. J., Rawlings, C. J., 1997, Nucleic acid and Protein Sequencing analysis,:A practical Approach, IRI Press, Oxford
3.
BNishop, M. J., 1998, Guide to Human genome computing, second Edition, Academic Press, London.
4.
David W Mount, 2004, Bioinformatics: Sequence and Genome Analysis, CSHL PRESS.
5.
Des Higgins, Willie Taylor, 2003, Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach, OXFORD UNIV PRESS.
6.
Per Jambeck, Cynthia Gibas, 2001, Developing Bioinformatics Computer Skills, O' REILLY publications.
MOLECULAR MODELLING AND COMPUTER-AIDED DRUG DESIGN
Unit I
Introduction to the concepts of molecular modeling structure design of artificial membrane. Molecular structure and internal energy. Application of molecular graphics: Energy minimization of small molecules; Empirical representation of molecular energies. Use of force fields and the molecular mechanics methods. Discussion of local and global energy minima.
Unit II
The Hartree-Fock equation. The techniques of molecular dynamics and Monte-Carlo Simulation for conformation analysis. Ab initio, dft and semi empirical methods. Quantum mechanical models.
Unit III
Macromolecular modeling. Design of ligands for known macromolecular target sites. Drug-receptor interactions. Classical SAR/QSAR studies and their implications to the 3-D modeler, 2-D and 3-D data base searching-pharmacophore identification and novel drug design with least side effects. Pharmacokinetic studies.
Unit IV
Structure-based drug design, Mechanism of their action, Enzyme inhibition strategies.
Unit V
Structure of commonly used drugs in clinical laboratory finding new drug targets to treat disease, new targets for anti-cancer drugs. Modification of receptor size and hormonal regulation, signal transductions. Multiple drug resistance.
References
1.
Andrew, R., 1998, Molecular modeling: principles and Applications, Leach, Harlow.
2.
Andrew, R., 1997, Molecular modeling: Basics and Applications, Hans-X
3.
Claude Cohen, N., 1999, Guidebook on molecular modeling in drug design.
4.
Leo, A., Hoekma, D. H., 1992, Exploring QSAR-Hans-ch Corwin.
5.
Matthew, F. Schlecht, 1993, Molecular modeling on the PC
6.
Rauter, C., Horn, K., 1994, X-ray crystallography and drug design, Elsevier.
7.
William B. Smith, 1995, Introduction to the theoretical organic chemistry and molecular modeling.
8..
Yvonne, C, Martin, 2000, Designing bioactive molecules: three dimensional techniques and applications.
RESEARCH METHODOLOGY
Unit I
Analysis and identification of research requirements - prioritization of research areas. Review of the work done in identified areas - Time scheduling- Laboratory and field facilities- Research duration- choice of research topic- Methodology - procedure- Experimental design.
Unit II
Basic principles and applications of bioinstrumentation - Electrophoresis of proteins - Nature and under denaturing conditions- N and C terminal analysis of proteins - Peptide mapping - separation technique -Principles (HPLC, GPC, FPLC) and applications- Chemical modifications of proteins- Microscopic studies-demonstration and application- Hydrodynamic properties -Measurements and application.
Unit III
Electrophoresis of DNA - Linear, circular and super coiled - determination of Tm of nucleic acid- centrifugation methods- sedimentation velocity - sub-cellular fractionation and ultra centrifugation- spectroscopy Lambert's and Beer's law - UV spectroscopy, IR & NMR Spectroscopy.
Unit IV
Computer application in biology:
FASTA, BLAST, EMBL, Sequence analysis, Algorithms, phylogenetic tree, GEN SCAN
Alignments (Pair wise, Multiple), Swiss-Prot.
Unit V
Statistics
Chi square test, Anova analysis, Correlation and regression, Statistical software packages for bioinformatics
Text Books
1.
Bishop, M. J., 1998, guide to Human Genome Computing Second Edition, Academic Press, London.
2.
Connor, O., 1991, Writing successfully in science Horpercollins Academic, London.
3.
Day, R. A., 1992, Scientific English: A guide for scientist and other professionals, Oryx, Press, Phoenix.
4.
Suhai, S., 1994, Computational Methods in genome research, Plenum Press, New York.
Practical V- Molecular modelling and computer aided drug design
Molecular mechanism and Dynamics of Proteins.
Molecular mechanism and Dynamics of Nucleotides.
Molecular mechanism and Dynamics of Drug molecules.
Drug target identification in a Protein/Nucleotide Sequence.
Prediction of drug molecules from lead molecules.
Drug target interactions.
Practical VI- Biological databank and analysis
PDB and its analysis.
CSD System analysis.
Genbank
NCBI search
OMIM
Pub Med search
EMBL
BLAST and FASTA format
Alignments - (Pair wise and Multiple-CLUSTAL W&X)
SEMESTER IV
DATA WAREHOUSING AND DATA MINING
Unit I
Need for Data Warehousing - Data Warehouse, definition and characteristics - Data Warehouse architecture- Overview of Client/Server Architecture.
Unit II
Data Warehousing Components: Overall architecture -Data warehouse database - sourcing - Acquisition -Cleanup and Transformation Tools, Metadata, Access Tools, Data Marts, Data warehouse administration and Management, Information delivery system.
Unit III
Building a Data Warehouse: Design considerations, technical considerations and implementation considerations, benefits of data warehousing, data extraction, clean up and transformation tools.
Unit IV
Introduction to Data Mining - Data Mining Functionalities - Concept/class description, Association Analysis, Classification and prediction, Cluster Analysis, Outlier Analysis, Evolution Analysis.
Unit V
Classification of data mining systems - Major issues in Data Mining. Mining Association rules in Large Databases. Association Rule Mining, Mining multidimensional Association Rules from Relational Databases and Data Warehouses. Decision trees: How the decision tree works.
Text Books
1.
Alex Berson, Stephen j. Smith, 2001, Data Warehousing, Data Mining and OLAP, McGraw Hill Companies Inc.
2.
Jiawei Han, Micheline Kamber, 2001, data Mining-Concepts and Techniques, Harcourt India Pvt. Ltd., Morgan, Kaufmann Publishers.
3.
Mark Humphries, Michelle Dy, Michael W Hawkins, 1999, Data Warehousing: Architecture and Implementation, Prentice Hall Publication.
4.
Ralph Kimball, 1998, The Data Warehouse Life Cycle Toolkit, John Wiley and Sons Inc.
5.
Sean Kelly, 1997, Data Warehousing in Action, John Wiley and Sons Inc.
6.
Usama M. Fayyad, Gregory Piatetsky-Shapiro, Padhrai Smyth and Ramasamy Uthurusamy, 1996, Advances in Knowledge Discovery and Data Mining, MIT Press
