Bioinformatics and Cheminformatics detailed syllabus for Pharmacy (Pharma) for 2021 regulation curriculum has been taken from the Anna Universities official website and presented for the Pharma students. For course code, course name, number of credits for a course and other scheme related information, do visit full semester subjects post given below.
For Pharmacy 5th Sem scheme and its subjects, do visit Pharma 5th Sem 2021 regulation scheme. For Professional Elective-I scheme and its subjects refer to Pharma Professional Elective-I syllabus scheme. The detailed syllabus of bioinformatics and cheminformatics is as follows.
Course Objectives:
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Unit I
BIOINFORMATICS AND BIOLOGICAL DATABASES 9
Introduction and scope of Bioinformatics, DNA and protein sequences, genome and transcriptome, extracting, collecting and storing sequences; various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF, NBRF-PIR. Introduction to Biological Databases; nucleic acid sequence databases: GenBank, EMBL, DDBJ; protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL; repositories for high throughput genomic sequences: EST, STS GSS; Genome databases at NCBI, EBI, TIGR, SANGER; structure databases: PDB, NDB, PubChem, ChemBank. Identification and interpretation of patterns in sequences; sequence patterns: InterPro, Prosite, Pfam, ProDom; structure patterns: FSSP, DSSP.
Unit II
SEQUENCE ALIGNMENT 9
Pairwise and Multiple sequence alignments: basic concepts of sequence alignment, Use of pairwise alignments and Multiple sequence alignment for analysis of Nucleic acid and protein sequences and interpretation of results. Algorithms used in sequence alignments- Needleman– Wunsch algorithm & Smith–Waterman algorithm. Sequence-based Database Searches: BLAST and FASTA, various versions of basic BLAST. Dot plot, basic concepts of sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues; Scoring matrices: basic concept of a scoring matrix, PAM and BLOSUM series.
Unit III
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Unit IV
CHEMINFORMATICS 9
Introduction, history and applications of cheminformatics; Data and Databases, Accessing PubChem through a Webinterface, Programming Access to the PubChem Database. Representing Small Molecules on Computers, Connection Tables, Molecular Graph issues, Line notation, Structural Data files, Chemical Resolvers, Molecular Editors and Visualization. Database Resources, Database Management, Public chemical Databases, Data Organization in PubChem as Data Aggregator, Database Query. Searching Databases for Chemical Information, PubChem Web Interfaces for Text, Text Search in PubChem, Additional Data Retreival in PubChem, Searching PubChem using a non-textual query, Programming topics.
Self study: Fundamentals of network and graph theory, cluster analysis, machine learning, data mining, big data in biology.
Unit V
ADVANCED CHEMINFORMATICS 9
Quantitative Structure-Property Relationships, Similar-Structure, Similar-Property Principle, Molecular Descriptors, Molecular Similarity, Similarity Coefficients. Computer-Aided Drug Drug Discovery Design (CADDD), Virtual Screening and Molecular Docking. Physicochemical parameters, Chemical reaction prediction and synthesis design.
Self study: Open source tools, techniques, data in cheminformatics, simulation and predictive tools, applications
Text Books:
- Introduction to Bioinformatics by Lesk, Arthur M., Oxford University Press
- Algorithms on Strings, Trees and Sequences by Dan Gusfield, Cambridge University Press.
- Biological Sequence Analysis Probabilistic Models of proteins and nucleic acids by Durbin, S.Eddy, A.Krogh, G.Mitchison.
- Bioinformatics Sequence and Genome Analysis by David W. Mount, Cold Spring Harbor Laboratory Press. Media.
- Thomas Engel , Johann Gasteiger, Chemoinformatics: Basic Concepts and Methods, ISBN: 978-3-527-33109-3
- Andrew R Leach and Valerie J. Gillet. (2007). Introduction to Chemoinformatics. Springer publications
Reference Books:
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Course Outcomes:
- Have the knowledge of the basic ligand/structure based drug design approaches.
- Understand the basic algorithms used in the established software to carry out the most common CADD project.
- Understand the importance of proper use of various parameters in cheminformatics application programs.
- Practical use of various computational tools available for computer aided drug design including 2D/3D structural database.
- identify cheminformatics problems that are suitable for applying machine learning techniques
- Know the kinds of descriptors available for chemical structures
For detailed syllabus of all the other subjects of Pharmacy 5th Sem, visit Pharma 5th Sem subject syllabuses for 2021 regulation.
For all Pharmacy results, visit Anna University Pharma all semester results direct link.