Semester-II Paper-VI: Computer Aided Drug Designing (CADD) Section A Introduction to Drug Designing: Process of Drug discovery, Drug

designing approaches: Target based, Ligand based and De Novo Drug Designing. Pharmacophore deduction and modeling, Analysis and Design of Combinatorial Libraries, Drug receptor interactions, Section B Representation and Manipulation of 2-D Molecular Structures: Introduction, Computer representation of Chemical Structures, Structure Searching, Substructure searching, Reaction Databases, representation of Patents and Patent Databases, 3-D Pharmacophores and Methods to derive 3D Pharmacophores. Drug designing softwares: Autodock, Ligbuilder, Molegrow. Section C Basic principles of Docking, Virtual Screening: Introduction, Structure Based Virtual Screening- Protein Ligand Docking, Scoring Functions for Protein Ligand docking, Practical aspects of structure based Virtual Screening; Prediction of ADMET Properties, 2 D and 3D data searching, Chemical databases, Role of computers in Chemical Research. Section D QSAR: Basic concepts, Objectives of QSAR, QSAR design and experimentation, QSAR descriptors and types, CoMFA and CoMSIA. SMILES (Simplified Molecular Input Line Entry Specification) Role of computers in Chemical search.

Suggested Readings: 1. Molecular Modeling for Beginners by Allan Hinchkliffe. 2. Combinatorial Library Methods and Protocols edited by Lisa B. English. 3. Molecular Modeling : Basic Principles and applications by Gerd Folkers, Wolfgang sippl, Didier Rognan, Hans Dieter(EDT) Holtje- Science-2003 4. Gupta S.P. Quantum Biology, New Age, 1996. 5. Essentials of Drug Designing by V. Kothekar, Dhruv Publications.

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Paper-VII: Computational Biology Section-A Computational methods for Gene Prediction: Gene Prediction in Prokaryotes and eukaryotes: content based, signal based, homology based and comparative based methods. Detection of Open Reading frames, machine Learning and probabilistic Method, Artificial neural network, hidden markov Model, Gene prediction algorithm. Section-B Promoter and Regulatory element prediction: Promoter and regulatory elements in prokaryotes, Promoter and Regulatory elements in eukaryotes, prediction algorithms: Ab Initio algorithm, phylogenetic footprinting based methods, expression profiling based methods. Transcription factor binding Sites, Splice site recognition methods, analysis of membrane proteins-hydropathy plots, TransFac, PSORT, Pfam, Prosite, rVISTA, Gensplicer. Section-C Principle of X ray Crystallography, NMR, Methods of single X ray diffraction of macromolecule-Molecular replacement Method and multiple isomorphous replacement method and direct method, fibre Diffraction. Methods for prediction of secondary structure of proteins: Ab initio based methods and homology based methods. Methods for prediction of tertiary structure of proteins: homology modeling, threading, fold recognition, Ab initio based methods. Secondary Structure analysis of RNA: Types of RNA structure, RNA fold algorithm, MFOLD, SFOLD, Vienna RNA Package. RNA secondary structure prediction method: ab initio, dot matrix, dynamic programming. Section-D Molecular interactions of Protein-Protein: Protein DNA, Protein carbohydrates, protein ligand,Protein protein Interaction databases: BIND, DIP, GRID, STRING, KEGG, MetaCyc, EcoCyc. Prediction algorithm for pathways and interaction: Gene Neighbourhood, Phylogenetic Profile, Gene Fusion, in silico two hybrids. Suggested Readings: 1. Setubal Joao and Meidanis Joao.Introduction to computational molecular Biology,PWS Publishing Company(An International Thomsaon Publishing Company),(1997)Indian low priced edition 2. Bioinformatics: sequence and Genome Analysis, by David Mount, second Edition.Cold Spring harbour labortory press(2004) 3. Discovering Genomics,Proteomics and bioinformatics,2/E by A.Malcolm Campbell and Laurie J.Heyer,Publisher:Benjamin Cummings(2007)

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paper VIII: System Biology Includes the basics of analysing metabolic pathways using bioinformatics tools and also the simulation of cellular environment. Goals: To understand the gradual maturation of genomics and proteomics into biology insilico. Convergence of genomics, proteomics, transcriptomics and metabolomics in to phenomics. Objectives: Students should be able to understand the interaction within biological networks and simulation of cells. Section- A Introduction to Systems Biology with all regulatory networks of metabolic pathways: What is systems biology? Integrating Networks. Methods of study: Micro array definition, types of array, micro array analysis: Hierarchical clustering, Self- organizing maps. Applications of micro arrays in system biology. Metabolomics & Metabolic Pathways Digestion of proteins and protein metabolism, Transport metabolism, Carbohydrate metabolism glycolysis, TCA cycle, PPP, glycogenesis, glycogenolysis, gluconeogenesis, PPP, ETC, Translating biochemical pathways into linear algebra. Section- B Whole cell simulation Principle and levels of simulation, Virtual erythrocytes, Pathological analysis, Fermentation analysis , Flux balance analysis, Minimal gene complement. Section- C Relationship analysis Predicting ligand binding function, Guilt by association, Use of gene cluster Comparative genome analysis, Binding surface comparisons, Detecting protein - protein interaction. Section -D Creative Bioinformatics Novel use for database, Use of EST database Unigene, Gene discovery, Primer design Restriction mapping, Pharmacophore building, Position specific cloning, SNP database, Target identification, Epitope identification REFERENCES 1. Bioinformatics A Practical Guide to the Analysis of Genes and Proteins. Ed. Andreas
D. Baxevanis and B. F. Francis Ouellette. John Wiley & Sons, Inc., Publications (For

Micro array). 2. Shanmughavel, P. 2006. Trends in Bioinformatics, Pointer Publishers, Jaipur, India.
3. The underlying pathway structure of biochemical reaction networks. Christopher H.

Schilling et. al. 1998. PNAS. 95:4193-8 4. Towards metabolic phenomics: Analysis of Genomics Data Using Flux Balances. Christopher H. Schilling et. al. 1999. Biotechnology. Prog. 15: 288-295.
5. The Minimal Gene Complement of Mycoplasma genitalium. Claire M. Fraser et. al.

1995. Science, 270: 397- 403.

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Paper-IX: Data Structure Algorithm

Section A Design principles :Data Structures and Algorithms, Object-Oriented Design Principles Analysis techniques: Running Time, Pseudo-Code, Quick Mathematical Review, Analysis of Algorithms, Asymptotic Notation: The ``Big-Oh'' Asymptotic Analysis Stacks, Queues, Lists: Stacks, Queues, Linked Lists, Double-Ended Queues Section- B Sequences: Ranked Sequences, Positional Sequences, General Sequences. Case Study: Bubble-Sort on a Sequence. Trees: The Tree Abstract Data Type, Basic Algorithms on Trees, Binary Trees, Data Structures for Representing Trees. Priority Section-C Queues: The Priority Queue Abstract Data Type, Priority Queue as a Sequence, Heaps. Dictionaries: The Dictionary Abstract Data Type, Binary Search Trees, AVL Trees, Hash Tables Section-D Sets, Sorting, Selection : Sets, Sorting: Merge Sort, Quick Sort, Radix Sort, Complexity of Sorting, Selection, Graphs, The Graph Abstract Data Type, Data Structures for Graphs, Graph Traversal, Directed Graphs, Strings, The String Abstract Data Type, Brute-Force String Pattern Matching, Regular Expression Pattern Matching Tries 1. V. Rajaraman, Fundamentals of computers (2ndedition), Prentice Hall of India, New Delhi, 1996. 2. B.Ram, computer fundamentals, Wiley, 1997. 3. Programming in C by Balagurusami. 4. let us C by Yaswant Kanitkar.

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Paper- X Java Programming & Data Mining Section A Object Oriented Concept, Introduction to Class, Object, Abstraction, Encapsulation, Polymorphism, Importance of Java, Data Types, Variables, arrays. Operators: Arithmetic, Relational, Logical, Unary, Conditional Operators. Control Statements, Creating Classes, Declaring Objects, Methods, Access Specifiers. Constructor: Introduction to Constructor, Method with Argument Passing, Method Overloading, Constructor Overloading. Section B Inheritance: Inheritance Basics, Types of Inheritance, using Super to Call Super Class Constructor, Interface Defining, Implementing Interface, Abstract Classes Final with Inheritance, Final to Prevent Overloading. Exception Handling: Using Try & Catch, Multiple Catch Classes, throw, final, Built own Exception. Section - C I/O Applets: Applet Basics, Applet Classes, Applet Life Cycle, Calling Applet with Parameters, Difference b/w application and Applet, Applet Paint, Repaint, draw line, Rectangle, Oval, String using Applet, Stream: Stream Basics, Byte Streams, Character Streams, Reading Congeal Input, Interface with AWT. Section D Data Mining: Data Mining Basics, Knowledge Discovery in Databases, Architecture of Determining, Decision Tree, Transactional Database, Data Warehouse Database. Introductory Data Security Concept. Discretionary and Mandatory Access Controls, Secure Architecture, Secure Transactional processing. Recommended books: JAVA 2: The Complete Reference by Patrick Naughton, Herbert Schidt, Osbourne Publishing; 3rd Edition. 1. 2. Teach Yourself JAVA in 21 Days Publisher: Sams net BK & CD ROM edition. 3. Data Minig Techniques by Arun K. Pujari, Publisher: University (India) Press Private Limited. 4. Data Mining Concepts & Techniques by Jaiwei Han and Micheline Kamber, Publisher: Elsevier, 2nd Edition.

SEMESTER III Paper-XI : Functional and comparative genomics Section-A Organization and Structure of Genomes: Genome Size, Sequence Complexity-Intron and Exons, repetitive Content of eukaryotic genome.DNA sequencing: Maxam Gilbert Method, Sangers Method, Automated DNA sequencing. Genome Sequencing Strategies: Hierachical (Clone contig) and shotgun method. Section-B Genome Sequencing: Genetic, Physical, cytological. Polymorphism, molecular markers - RFLP, VNTR, AFLP, SSR, RAPD. SNP, SNP detection methods-SSCP, PCR based, DGGE, TGGE, SNP diseases, SNP databases-dbSNP, Pharmacogenomics, Pharmacotherapeutics.Use of SNP information in pharmacogenomics and personalized medicine. Section-C Objective and Overview of Genome Comparisons, Genome Alignments, BLAST2, Mummer, Pip Maker,VISTA, Comparison of Gene Order, Gene Order, Comparative Genomic, Viruses, Microbes, Pathogens, Eukaryotes, Comparative Genomic Databases, COG, VirGen, CORG, HOBACGEN, Homophila, XREFdb, Gramene. Section -D Evolution of genomes, horizontal gene transfer, comparative genomics of Eukaryotes, genomes of Saccharomyces cervisiae (baker's yeast), Caenorhabditis elegans, Drossophila melanogaster (Fruit fly), Arabidopsis thaliana etc. Suggested Readings: 1 Setubal Joao and Meidanis Joao.Introduction to computational molecular Biology, PWS Publishing Company (An International Thomson Publishing Company), (1997) Indian low priced Edition harbour Laboratory Press (2004). 2 3 Bioinformatics: sequence and Genome Analysis by David Mount, second Edition. Cold Spring Discovering Genomics, Proteomics and Bioinformatics,2/E by A. Malcolm Campbell and Laurie J.Heyer, Publisher :Benjamin Cummings(2007)

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Paper-XII: Metabolomics and Proteomics Section-A Introduction to Biochemistry with a metabolomics / regulation approach; the alphabet of biochemistry, pKa, pH, and buffers. Review of energetics; free energy, steady state. Review of enzyme kinetics, regulation approach (By KEGG Pathway) analyzing Metabolomic data from glycolysis/fermentation; regulatory analysis case study on cancer cell metabolism, Citric Acid Cycle with anaplerosis and glycoxylate cycle, Pentose phosphate shunt, Gluconeogenesis and glycogen biosynthesis, Fatty acid anabolism connections to central metabolism, Synthesis of cholesterol and steroid hormones, connections to central Metabolism, nitrogenous compound-related biochemical pathways, Section-B Amino acid biosynthesis and catabolism, Nucleotide biosynthesis and catabolism, Metabolomics and regulation of amino acid and nucleotide pathways; genetic diseases affecting amino acid and nucleotide metabolism and their regulatory implications, case studies Catabolism of polynucleotides, Anabolism of proteins, Catabolism of proteins, Global regulation of nucleotide and protein macromolecular synthesis, regulation of turnover, genetic diseases and antibiotics affecting anabolism or catabolism of macromolecules. Section-C Introduction to proteomics, Analysis of proteome-2D PAGE: Sample preparation, solubalization, reduction, resolution, reproducibility (overview only) Mass Spectrometry based methods for protein identification: De novo sequencing using Mass spectrometric data, use of MALDI TOF and related methods for protein mass determination. Determination of Protein structure: Edmann Degradation Section-D Protein: Determination of sizes (Sedimentation analysis, gel filtration, SDS PAGE, Native PAGE). Post Translational modification: Methylation, Glycosylation, lipid attachment and disulphide bond formation. Protein Protein Interaction: FRET, Yeast Two Hybrid, co-immunoprecipitation Suggested Readings: 4 Setubal Joao and Meidanis Joao.Introduction to computational molecular Biology, PWS Publishing Company (An International Thomson Publishing Company), (1997) Indian low priced Edition harbour Laboratory Press (2004). 5 Bioinformatics: sequence and Genome Analysis by David Mount, second Edition. Cold Spring 6 Discovering Genomics, Proteomics and Bioinformatics,2/E by A. Malcolm Campbell and Laurie J.Heyer, Publisher :Benjamin Cummings(2007)

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Paper-XIII: Gene expression and Microarray analysis Section A

Why are MicroArray Important? What is a DNA MicroArray. Designing a MicroArray Experiment: The Basic steps, Types of MicroArray, NCBI and MicroArray Data Management, GEO (Gene Expression Omnibus), MAML, The benefits of GEO and MAML. K-Means Clustering, Hierarchical Clustering, Self Organization Maps (SOM). Identifying Genes: Expressed usually in a sample, Classifying Samples from two populations using Multilayer Perceptron, Support Vector Machines and their applications, Using genetic algorithm and perceptron for feature selection and supervised classification.

Section B Introduction to ESTs, ESTs clustering assembly and EST databases, Alternative splicing, Differential display, Regulatory RNA: SnRNA, microRNA, SiRNA, RNAi, antisense RNA technology, Secondary structure analysis of RNA: Stem and Loop structure, Section C Comparative Genomics: Homologous: Orthologous and Paralogous, Analogous, Xenologous, Horozontal gene transfer. Orthologous identification BLAST and Reciprocal Best Hit, Cluster of Orthologous Groups, Synteny, Gene Order, Phylogenetic footprinting, Use of comparative genomics in gene annotation and function prediction. Section D Web based servers and softwares for gemone analysis: Ensembl, UCSC and NCBI genome browsers, Large genome alignments: Problems of complexity, reapeats and size. Recommended Books: 1. Bioinformatics: Sequence and Genome Analysis, by David Mount, Second edition, Cold Spring Harbor Laboratory Press(2004) 2. Discovering Genomics, Proteomics and Bioinformatics, 2/E by A. Malcolm Campbell and Laurei J. Heyer, publisher: Benjamin cimmings(2005) 3. Proteins: Structures and Molecular Properties by T.E. Creighton.W.H.Freeman & Company 2nd Edition, 1993. 4. Microarray Bioinformatics by Dov Stekel, Published by Cambridge University Press, 1st Edition, 2003.

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Paper-XIV: Molecular Structure Prediction and Visualization Section A Concepts of Molecular Modeling, Coordinate System: Cartesian and Internal, Surfaces, Potential Energy Surfaces, Molecular Graphics and Structure visualization, Applications of Molecular Graphics in Molecular Modeling. Force Fields: Molecular mechanics and Quantum mechanics, Features of Molecular mechanics force fields. Bond stretching, Angle bending, Torsion terms, and Non- bonded interactions: Electrostatic interaction, Vander walls interactions, and Local and Global energy minima. Section-B Overview of Drug design, Simulation Methods, Molecular Mechanics, Monte Carlo, Semi-Impirical Method, Ab-inito Method. Analog based drug design: QSAR, Molecular Structure determination, Advance crystallographic techniques, Simulation Anneling (Autodock /Quantum), Peptide, Comparative Protein, Modelling: Homology Modeling, Structural Alignment, Ramachandran plot (Side Chain Placement Refinement & Validation of Model), 3D- Pharmacophore modeling. Section C Energy minimization methods: Derivatives and Non derivatives methods, Applications of energy minimization, Energy minimization by Systematic search. Molecular Dynamics: Methods and simulations, Monte Carlo method, Difference between Molecular dynamics and Monte Carlo method. Section D Quantum mechanical methods: Schrdinger equation, molecular orbital calculations, Hartree Fock Method, semi-empirical methods. Suggested Readings: 1. Molecular Modeling for Beginners by Allan Hinchkliffe. 2. Combinatorial Library Methods and Protocols edited by Lisa B. English. 3. Molecular Modeling : Basic Principles and applications by Gerd Folkers, Wolfgang sippl, Didier Rognan, Hans Dieter(EDT) Holtje- Science-2003 4. Gupta S.P. Quantum Biology, New Age, 1996. 5. Essentials of Drug Designing by V. Kothekar, Dhruv Publications.

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Paper-XV PERL and My SQL in Bioinformatics PERL programming: An Introduction, Perl features, Operators, Statements, Loops, Arrays, Arrays slices, Hashes, List Processing, File Handles, Pattern Matching. How to run perl programs in Linux/Windows environment, Error Message, Debugging, Perl interpreters, Perl scripts. Scalar values and scalar variables, Strings and numbers, Assignment statements, Blocks, Arrays, Hashes, Operators, Binding operators, Loops, IO, Input from file, Input from SDIN, Input from file named in command line, Regular expression, Pattern matching, Meta symbols, Pattern modifiers, Subroutines and modules, Builtin, functions. Section-B Application of Perl in Bioinformatics: Representing strings and sequenced data in Perl, Program to store a DNA sequence, Concatenating DNA fragments, DNA to RNA transcription, Reading proteins from files, Finding motifs, Counting nucleotides, Exploding strings into arrays, Operating on strings. Section-C A program to simulate DNA mutation, Generating random DNA, Analyzing DNA, Translating DNA into proteins, GenBank sequence and annotation, Parsing annotation, Indexing GenBank with database. PDB files, Parsing PDB files, Parsing BLAST output, Introduction to BioPerl, CPAN. Introduction to MATLAB. Section-D Introduction to database, Entity set, ER model, Network model and Hierarchical model, Relational model. SQL Select statements; Data definition statements, Data manipulation statements, Data control statements, Other database objects (Views, Sequences, and Synonyms), DDL table: create, alter, and drop, DML: Record, insert, delete, update and truncate, Keys: primary, foreign, unique, check, default, candidate, alternate. Suggested readings: 1. An introduction to database system by C J Date Pearson Education 2. Oracle SQL complete Reference by Tata McGraw Hill 3. Mastering Perl for Bioinformatics by James Tisdall.

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SEMESTER IV Elective I: Pharmacogenomics Section-A INTRODUCTION TO PHARMACOGENOMICS Pharmacogenomics: Historical perspectives and current status, Human Genome and Genomic Applications, Genetic Polymorphism of Metabolic Reactions, SNPs, Association Studies in Pharmacogenomics, Study on industries developing pharmacogenomic research. FUNCTIONAL ANALYSIS OF GENE VARIATION: Transfection Assays With AlleleSpecific Constructs: Functional Analysis of UDP-Glucuronosyltransferase Variants, CYP 2D6, CYP2C19 in drug metabolism, Snapshot of the Allele-Specific Variation in Human Gene Expression, Genome-Wide Analysis of Allele-Specific Gene Expression Using Oligo Microarrays, Roche Ampli Chip, HaploChIP: An In Vivo Assay. Section -B GENOTYPING TECHNIQUES Aspects Influencing Genotyping Method Selection, Denaturing HPLC for Mutation Detection and Genotyping, Pyrosequencing of Clinically Relevant Polymorphisms, Kinetic Fluorescence-Quenching Detection Assay for Allele Frequency Estimation, MALDITOF Mass Spectrometry, Fluorescence-Based Fragment Size Analysis, SNP Genotyping in DNA Pools, Genotyping of InDel Polymorphisms Section C PHARMACOGENOMICS IN PERSONALIZED MEDICINE Pharmacogenomics of Cardiovascular Diseases, Pharmacogenomics of Cancer treatment, Pharmacogenomics of Neurodegenerative Diseases, Pharmacogenomics in Depression, Pharmacogenomics and Respiratory diseases, Pharmacogenoomics in AIDS, Pharmacogenomics in Antibiotics. Section D MANAGEMENT OF PHARMACOGENOMIC INFORMATION The Pharmacogenetics and Pharmacogenomics knowledge Base, Systems for the Management of Pharmacogenomic Information Suggested Readings 1. Werner Kalow, Urs B.Meyer, and Rachel F. Pharmacogenomics, Second Edition (Drugs and the Pharmaceutical Sciences), Tyndale, 1st Edition, Publisher CRC. 2. Federico, MD Pharmacogenomics: Methods And Applications (Methods in Molecular Biology, Ph.D., Innocenti, Published by Humana Press. 3. Julio Lianio Ma- Li Wong Pharmacogenomics: The search for individualized Therapies, Wiley-VCH Publisher. 4. Dhanoa, DS Pharmacogenomics in Drug Discovery and Development (Drug Discovery Series) , 1st Edition, CRC Publisher.Michael, G Catania, S An A-Z Guide to Pharmacogenomics, Sci-Tech Book news.

Elective II Visual Basic and Web enabling Technology SECTION A Introduction to HTML, Structure of HTML Pages, Text formatting Tags, adding graphics with image tag, Image element attributes, using image as links, creating internal and external links. Tables: Presenting information in tables, frameset, table as lay out tools, nested tools. Frames: using frames, frameset, target links, no frame element. Forms: using HTML forms, input control elements and attributes, processing forms. SECTION B Basic of active server pages, introduction of ASP Objects, writing server-side code using components, accessing database with ASP and ADO, ASP, Application advanced ASP, beyond asp. SECTION C XML - Introduction, anatomy of XML document, using xml markup, working with elements and attributes, checking well formedness. XML objects exploiting entities, checking validity creating xml links, viewing xml in internet explorer, viewing xml in other browsers, even-driven programming styling xml with CSS. SECTION D Introduction to application development using Visual Basic. Variables, standard controls, working with code and forms. Data access using data control. Suggested readings: 1. 2. 3. 4. 5. Active Server pages teach yourself in 21 days. XML for Bioinformatics by Ethan Cerami. XML teach yourself in 21 days, published by SAMS Techmedia. Visual Basic published by Schaums Outline. Mastering in Visual Basic 6.0 Published by BPB.

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