M.PHIL. BIO -INFORMATICS
CURRICULUM
Sl.No
Papers
Max. Marks
Ex. Hrs.
1
Research Methodology
100
3
2
PROTEOMICS AND GENOMICS
100
3
3
MOLECULAR MODELING AND DRUG DESIGNING
100
3
4
Dissertation
100
-
PART-1
RESEARCH METHODOLOGY FOR BIO INFORMATICS
SYLLABUS
UNIT I
Research : Definition, Importance and meaning of research, Types of research, Steps followed for research. Identification,
Selection and formulation of research problem. Research questions, Research design. Formulation of hypothesis. Review of literature.
UNIT II
Sampling techniques: Sampling theory, types of sampling, steps in sampling and non sampling error, Sample size,
Advantages and disadvantages in sampling.
Collection of Data : Primary data, Data collection method used, Secondary Data, meaning, relevance’s, limitations and cautions.
UNIT III
Biological data : Classification of biological databases. Protein sequence databases, Nucleotide databases, Structure
databases, Specialized databases, derived databases. Uses and applications of derived and specialized databases.
UNIT IV
Sequence similarity searches. Scoring Matrices. Alignment: Pair wise and Multiple Sequence Alignment. Tools: BLAST,
FASTA and CLUSTAL W. Dynamic Programming. comparative analysis by Pair wise alignment.
UNIT V
Genome database: HGP – Organization, history, accomplishment and the data manipulation. Mouse Genome Database,
?Yeast Genome Database, BACs, Online Mendelian Inheritance in Man and KEGG,TIGR,MBGD
UNIT VI
Statistics in research- Measure of central tendency. Dispersion, Skew ness and Kurtosis in research. Hypothesis –
Fundamentals of hypothesis testing – Standard error. Point and interval estimates. Important non-parametric tests: Sign, Run, Kruskal
– Wallis tests and Mann – Whitneys test.
UNIT VII
Parametric tests: Testing significance_ mean, Proportion, variance and correlation.
Testing for significance of difference between means, proportions, variances and correlation coefficient. Chi-square tests. ANNOVAOne way and Two way.
UNIT VIII
Research report: Types of Reports, contents, styles of reporting . Steps in drafting reports, Editing the final draft.
Evaluating the final draft.
REFERENCE BOOOKS:
1.
Statistical Methods – S.P. Gupta
2.
Research Methodology Methods and Techniques – C.R.Kothari
3.
Statistics – Theory and theory – B.N. Gupta
4.
Research Methodology Methods and Statistical Techniques – Santhosh Gupta
5.
Introduction to Bioinformatics - Attwood
6.
Bioinformatics: Sequences and Genomes: David W Mount
PAPER II
PROTEOMICS AND GENOMICS
UNIT I
Chemical foundation of cell – molecular weight, mass and their correct units – genetic foundations –
evolutionary foundations. Amino acids – absorption of light by molecules – peptides and proteins - working with
proteins – covalent structure of proteins – investigating protein with Mass Spectroscopy – Protein sequencing and
evolution.
UNIT II
3D structure of protein: Overview – Protein secondary, tertiary and quaternary structure – protein
denaturation – protein folding – reverse turns. Protein interaction modulated by chemical energy: actin, myosin and
molecular motor. Protein metabolism: genetic code – protein synthesis – determination of size of proteins.
UNIT III
Gene organization and expression: General principle of gene organization and replication – Common features
of prokaryotic and Eukaryotic gene expression – characteristics of gene expression – transcription – splicing –
chromosome structure.
UNIT IV
Ribonomic – Genomes and Genomics – Pattern of genome organization – nenome packaging – Genome
stability – Genome Instability – Genome flexibility
UNIT V
Genome evolution – Genome and their mapping – Paattening genetically engineered organisms
UNIT VI
Sequencing of proteins – N and C terminal sequencing – Protein chip – Expasy proteomics – Current trends
in expression proteomicsUNIT VII
Application Proteomics: To drug development and toxicology, Mixing Proteome, Protein expression profile,
UNIT VIII
Application of Human genetic research – gene modifications and food uses – genetically manipulated
organization to the environment – stem cells – therapeutic and regenerative medicine.
TEXT BOOKS:
1. Proteomics: from protein sequence to function. Edited by S.R. Pennington & M.J. Dunn. Published by viva
books (2002).
2. Introduction to Proteomics: Tools for the new biology by Daniel C. Liebler published by Humana Press.
(2002).
3. Biochemistry, Wilson and Walker.
4. Genomes, T.A. Brown
5. Genetic Engineering, J. williams, A. cecceralli and A.wallace, 2 nd edition, bios publishers, 2001.
6. Genomics and cloning technology and application, HD Kumar, East West Press.
REFERENCES:
1. Wilkins M.R., Williams K.L., Appel D.F., Hochstrasser (eds) 1997. Proteome Research: New Frontiers in
Functional Genomics Springer – Verlag Berlin Heidelberg.
2. Bentley D.R., in Genomics (eds Dixon G.K., Coppin L.G and Living Stone D), Bios Scientifics,
3. Bauw, G. and Monatgu, M.V., in Differentially expressed genes in plant: A bench manual (eds Hanse, E and
harper G) , Taylor and Francis,
4. T.A. Brown, Genomes, 2nd edition, BIOS Scientific Publishers, Ltd., Oxford.
5. David W. Mount, Bioinformatics – Sequence and Genome analysis, Cold Spring Harbor Laboratory Press
6. Eugene V. Koonin and Michael Y. Galperin, Sequence, Evolution Function, Computational Approaches in
Comparative Genomics, Kulwer Academic Press.
Paper-III
MOLECULAR MODELING AND DRUG DESIGNING
SYLLABUS
UNIT I
Atomic structure, molecular theory for polyatomic molecules; valence states and hybridization; Computer
Simulation Methods. Time averages and ensemble averages; molecular dynamics method the basic elements of the
Monte Carlo method. Calculation of simple thermodynamic properties; Monte Carlo simulation Methods. Calculating
properties by integration; implementation of the Metropolis Monte Carlo method;
UNIT II
Quantum Mechanical Method; ab initio and semi-empitical approaches. Molecular Mechanics. Molecular
mechanics force field; features calculating thermodynamic properties using a force field.
UNIT III
Molecular dynamics Simulation Method. Molecular dynamics using simple methods; conformational changes
form molecular dynamics simulations; basic principles of protein structure; the hydrophobic effect first principles
methods for predicting protein structure; lattice models for investigating protein structure; Rule based approaches;
homology and comparative modeling methods.
UNIT IV
Drug discovery: Overview of the drug discovery process,, Modern methods of drug discovery, Various
phases- Drug discovery pipeline, Economics of drug discover, Stages and strategies of drug discbvoery6, Rational
approach in Drug design, Computer aided drug design, success stores. Scenarios: Combinatorial chemistry, 3D
pharmacophore hypothesis, Structure based drug design, De-novo design techniques.
UNIT V
Structure based drug design; Molecular targets and pathways relevant to disease processes; Receptors,
channels, transporters and enzymes as drug targets; Role of protein 3D structures in the drug discovery process,
Techniques for protein structure prediction- Comparative modeling, structural genomics. Design of combinatorial
libraries, selection of subsets for HTS and hit validation, Lead optimization and candidate selection.
UNIT VI
QSAR: 2D-QUAR; 3D-QSAR, Examples CoMFA and CoMSIA. Physiochemical concepts in drug design;
Physiochemical and biopharmaceutical properties; Experimental approaches, solubility, Liphophilicity, absorption
models; Computational approaches.
UNIT VII
Success stores of protein structure based drug design- X-Ray structure based drug design, Homology model
based drug design. Application of protein structure information in the drug discovery process.
UNIT VIII
Applications of modeling in the SBDD, Substrate binding sites, Applications in combinatorial libraries and
2D and 3D database searching;
TEXTBOOKS
1. Molecular Modeling, Principles & Applications, Andrew R.Leach,
2. Addison Wesley Longman, Singapore, 1996
3. ‘Modern Methods of Drug Discovery’ by Gerhard Edwin Seibold, Alexander Hillisch, Rolf Hilgenfeld
Publisher
4. “Advanced Drug Design and Development” Kourounakis Taylor and Francis.
References
1.
2.
3.
4.
5.
Basic Inorganic Chemistry, F.A. Cotton & G. Wilkinson, Wiley Eastern, New Delhi (for unit I)
“Drug Design: Cutting Edge Approaches”. Angewandte Chemie, International Edition, Vol.42,
“Biopharmaceutical Drug Design and Development”. Susanna Wu-Pong and Yongyut Rojanasakul,
“Pharmacokinetics & Metabolism in Drug Design”. D.A. Smith, H.van de Waterbeemd & D.K. Walker
(Eds). John Wiley & Sons,
Notes on Molecular Orbital Calculations, J.D. Roberts, Benjamin.