SRM UNIVERSITY

FACULTY OF ENGINEERING & TECHNOLOGY

SCHOOL OF BIOENGINEERING
DEPARTMENT OF BIOINFORMATICS

BI0205- INTRODUCTION TO BIOINFORMATICS

LECTURE PLAN

Semester: III Course: Introduction to Bioinformatics

Code: BI0205 Staff Handling:Mrs. J.B.SHEEMA
Section: II. A Total Hours: 45

LECTURE TOPIC LEARNING OUTCOME

UNIT I-HISTORY, SCOPE AND
1 IMPORTANCE
Introduction to bioinformatics, history o Types of biological data and
Applications of bioinformatics related to its processing methods, its
2
various fields of biology outcomes
Challenges and opportunities in
3 o Knowledge of various online
bioinformatics
Role of computers in bioinformatics, applications used in
4 processing biological data
types of softwares used
Internet and its usage, types of online
5
servers used in bioinformatics
6 Introduction to EMBNET and NCBI
7
8
UNIT II- DATABASES, TOOLS AND
9 THEIR USES.
Introduction to Databases, types o Processing of Biological data
Nucleic acid sequence databases using IT tools
10&11
Protein sequence data bases o A thorough understanding of
12
various databases and data
Introduction to structural databases,
13&14
PDB, MMDB,CATH,SCOP o Significance of database
Introduction to bibliographic databases, searches
15
PUBMED, MEDLINE
Virtual library o Usage of database related
16 tools to search data

Standalone packages used in

17
bioinformatics
Advantages and disadvantages of
18
standalone packages
UNIT III- SEQUENCE
19 ALIGNMENT METHODS
Introduction to sequence analysis, types o Understanding Sequence
20 Methods of alignment. DOT PLOT analysis

Dynamic programming o To clarify basic concepts

21
(local and global alignment)
 22 Heuristic method. FASTA related to aligning sequences.

23 BLAST o Understand the uses of global

and local alignments
Introduction to scoring matrices and its
24
uses
o Usage of various alignment
Multiple sequence alignment, tools and
25 parameters to manipulate
methods
alignments in protein
Application of multiple sequence sequences.
26
alignment
Using MSA to retrieve meaningful o Methods of constructing
27
information in a protein--motifs multiple sequence alignments.
Comparing MSA and PSA
28
o Meaning of Motifs
UNIT IV-PREDICTING METHODS
USING DNA AND PROTEIN
29&30 SEQUENCES
Gene predictions strategies
o Types of predictive methods
Protein prediction strategies
31&32 o Understanding evolution

Types of softwares for predicting genes o Methods to predict genes and

33 their products
and their functions
Molecular visualization
34 o Distinguishing homology and
similarity
Meaning of Homology, difference
35
between homology and similarity
36 Phylogeny and relationships
37 Clustering, dendrogram and other graphs
UNIT V-DRUG DISCOVERY AND
38 PHARMAINFORMATICS
Introduction to Drug targets
39&40 Process of discovery of drug o Applications of Bioinformatics
in drug discovery
41 Target identification- steps
42 Target validation - steps, methods o Overview of drug discovery
43 Lead optimization – methods process
44 Concept of chemical libraries
45 Types of chemical libraries

TEXT BOOK
1. S.C. Rastogi and others, Bioinformatics –Concepts, Skills and Applications. CBS Publishing, 2003.
2. C. Ignacimuthu, S. J., Basic Bioinformatics, Narosa Publishing house, 1995.
REFERENCE BOOK
1. T. K. Atwood, D J Parry-Smith, Introduction to Bioinformatics, Pearson Education, 1st Edition, 11th Reprint
2005
2. C S V Murthy, Bioinformatics, Himalaya publishing house, 1st Edition, 2003.

Signature of HOD Signature of Staff

 DEPARTMENT OF BIOINFORMATICS
SCHOOL OF BIOENGINEERING
SRM UNIVERSITY
LECTURE PLAN
Subject code: BI0401 Credits: 3
Subject: Chemoinformatics Semester: VII A
Staff: Mrs.J.B.Sheema

Hour Contents Learning Outcome

1. UNIT 1 REPRESENTATION OF STRUCTURES
Introduction
2. • Introduction to
3. Chemoinformatics
Representation and Manipulation of 2D
4.
Molecular Structures
5. • Introduction to
6. various chemical
7. representations
Representation and Manipulation of 3D
8.
Molecular Structures • Knowledge on
9.
manipulation of 2D
and 3D chemical
structures
10. UNIT 2 MOLECULAR DESCRIPTORS AND
11. MODELS
Introduction • Knowledge on
Descriptors Calculated from the 2D Structure various molecular
12. Descriptors Based on 3D Representations‐ Data descriptors
13. Verification and Manipulation‐ Computational
Models
14. Deriving a QSAR Equation using Simple and • Derivation of QSAR
15. Multiple Linear Regression equation
16.
17. Designing a QSAR Experiment
• Regression methods
18. Principal Components Regression
19. Molecular Field Analysis , Partial Least Squares
20. • Knowledge on MFA
and PLS
21. UNIT 3 SIMILARITY METHODS
22. Introduction, Similarity Methods‐ Similarity • Knowledge on
Based on 2D Fingerprints‐ Similarity similarity and
23.
Coefficients‐ 2D Descriptor Methods dissimilarity based
24. 3D Similarity methods
25. Selecting Diverse Sets Of Compounds ‐ Cluster
 Analysis
26. Dissimilarity‐Based selection methods • Knowledge on
various optimization
27.
methods
28. Cell‐Based Methods
29. Optimization Methods
30. Comparison and Evaluation of Selection • Comprehensive
Methods ideas of the
methods studied
31. UNIT 4 HIGH THROUGHPUT AND VIRTUAL
32. SCREENING • Importance of
Introduction, Analysis of High‐Throughput screening methods
Screening Data, Data Visualization in
33. Chemoinformatics
Data Mining Methods
34.
35. Virtual Screening, Drug-Likeness and Compound
Filters
36. • Study on various
37. Structure‐Based Virtual Screening ADMET properties
38.
39. The Prediction of ADMET Properties
40. UNIT V COMBINATORIAL CHEMISTRY AND
LIBRARY DESIGN • Designing chemical
Introduction, Diverse and Focused Libraries libraries
41. Library Enumeration
42. Combinatorial Library Design Strategies
43. Approaches to Product‐Based Library Design • Examples of library
designing methods
44. Multi objective Library Design
45. Practical Examples of Library Design

TEXTBOOKS
1. Andrew R Leach, Valerie J Gillet, An Introduction to Chemoinformatics, Kluwer academic
publishers, 2003
2. Tudor I Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd Folkers, Chemoinformatics in Drug
Discovery, Wiley‐VCH, 2006

REFERENCE BOOKS
1. Johann Gasteiger, Thomas Engel, Chemoinformatics‐ A Textbook, Wiley‐VCH, 2003
2. Jürgen Bajorath, Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery,
Humana press, 2004

Signature of HOD Signature of Staff