Syllabus
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Course Code: MMB-401B Course Name: Computational Biology |
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| MODULE NO / UNIT | COURSE SYLLABUS CONTENTS OF MODULE | NOTES |
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| 1 | Genomics and Gene Annotation: Organization and structure of prokaryotic and eukaryotic genomes; Genome annotation and databases; Automated in-silico methods of finding gene and relevant features; Genome Sequencing using first and seconding generation sequencing methods; Advantages of genome sequencing projects in modern biological research. Genomics Analysis: Diversity and features of completed genomes: Viral, prokaryotic (E .coli) and eukaryotic genomes (Arabidopsis, Human). Codon bias and optimization. Primer designing. Gene prediction methods. Techniques used in genomics and transcriptomics: NGS, Microarray, RNAseq. |
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| 2 | Protein structure and proteomics: Hierarchy and features of protein structure: primary, secondary, tertiary and quaternary structures. Structural classes, motifs, folds and domains. Modelling of tertiary structure of protein in presence and absence of template. Energy minimizations and evaluation by Ramachandran plot. Proteome, interactome, 2-D gel electrophoresis, MALDI-TOF spectrometry, STRING, MMDB. Computer aided drug discovery. |
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| 3 | Protein Structure Databases: Different databases of macro-molecular biomolecules; Accessing and mining protein structure classification databases such as SCOP, CATH; Tools for viewing and interpreting macromolecular structures. Protein Structure Comparison: Various algorithms and programs for superimposition of structures; RMSD calculations, multiple structure alignment methods such as DALI and VAST. |
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| 4 | Protein Structure Prediction &Molecular Modeling: Principles of secondary and tertiary structure predictions; Ab-initio and homology based methods of secondary and tertiary structure predictions; Homology modeling; Threading and ab-initio protein structure prediction. Inferring Function from Protein Sequence &Structure: Using evolutionary information; Gene neighborhood; Phylogenetic profiles; Gene fusion; Catalytic templates; Prediction and analysis of binding cavities for function prediction. |
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