Bioinformatics and computational technology M.Pharmacy 2nd Semester 2022 (2021-2022) Previous Year's Question Papers/Notes Download - HK Technical PGIMS

BIOINFORMATICS AND COMPUTATIONAL BIOTECHNOLOGY
(MPB 203T)
Scope This paper has been designed to provide the advanced knowledge to the
biotechnology students in invaluable areas of advanced bioinformatics which
plays a crucial role in determining its future use and applications in medicine, drug discovery and in pharmaceutical industry. Objectives Upon completion of this course it is expected that the students will be able to
understand,  Use of computers in developing a new drugs  Biological concepts for bioinformatics  Proteins and their diversity  Various gene finding methods  Searching the biological databases  Target searching  Various methods of drug designing
THEORY 60 Hrs 1. Introduction to Bioinformatics Definition and History of Bioinformatics, Internet and
Bioinformatics, Introduction to Data Mining, Applications of Data
Mining to Bioinformatics, Biological Database Protein and nucleic acid databases. Structural data bases. Collecting and storing the sequence and Applications of
Bioinformatics.
12
Hrs
2 Sequence analysis Sequence alignment, pair wise alignment techniques, multiple
sequence analysis, multiple sequence alignment; Flexible
sequence similarity searching with the FAST3 program package, the use of CLUSTAL W and CLUSTAL X for the multiple
sequence alignment. Tools used for sequence analysis. 3 Protein informatics
Introduction; Force field methods; Energy, buried and exposed
residues, side chains and neighbours; Fixed regions, hydrogen
bonds, mapping properties onto surfaces; Fitting monomers, R &


S fit of conformers, assigning secondary structures; Sequence
alignment-methods, evaluation, scoring; Protein completion, backbone construction and side chain addition; Small peptide
methodology, software accessibility, building peptides; Protein
displays; Substructure manipulations, annealing. Protein structure prediction Protein folding and model generation; Secondary structure
prediction, analyzing secondary structures; Protein loop
searching, loop generating methods, loop analysis; Homology
modeling, concepts of homology modeling, potential applications, description, methodology, homologous sequence identification;
Align structures, align model sequence; Construction of variable
and conserved regions, threading techniques, Topology
fingerprint approach for prediction, evaluation of alternate models;
Structure prediction on a mystery sequence, structure aided
sequence techniques of structure prediction, structural profiles, alignment algorithms, mutation tables, prediction, validation, sequence based methods of structure prediction, prediction using
inverse folding, fold prediction; Significance analysis, scoring
techniques, sequence- sequence scoring. Docking
Docking problems, methods for protein- ligand docking, validation
studies and applications; Screening small molecule databases, docking of combinatorial libraries, input data, analyzing docking
results. 4 Diversity of Genomes Prokaryotic and Eukaryotic Gene Families. Genome Analysis:
Introduction, Gene prediction methods, Gene mapping and
applications- Genetic and Physical Mapping, Integrated map,
Sequence assembly and gene expression. Completed Genomes Bacterium, Nematode, Plant and Human
Evolution of Genomes Lateral or Horizontal Transfer among Genomes, Transcriptome
and Proteome-General Account
Phylogenetic analysis Evolutionary Change in Nucleotide Sequences, Rates and
Patterns of Nucleotide Substitution, Models for Nucleotide
Substitution, Construction of Phylogenetic Tree, Genome
Annotation technique.


5 Target searching and Drug Designing
Target and lead, timeline for drug development, target discovery, target modulators, In-silico gene expression, microarray, and lead
discovery, libraries of ligands, active site analysis, and prediction
of drug quality.