Course Syllabus

Each participant (student) needs to select two optional sections (out of four choices) in addition to ten compulsory sections. Each section has an allotted duration of 6 hrs.

Compulsory Sections (6 hrs each):

1. BiC1. Why Bioinformatics? Essential Recapitulations

   Introduction to Informatics and Data Science, Philosophy of Knowledge-based / semi-empirical approaches in biophysical and biological sciences in contrast to First Principle-derived / physics based approaches. Recapitulation of the first and second laws of thermodynamics. Recapitulation of basic calculus: differentiation and Integration. Recapitulation of basics of modern algebra and statistics: Set theory, Probability, Distributions, central tendencies and deviations, t-test & Chi square tests. ( 6 hrs )

2. BiC2. Algorithms and Networks

   Introduction to Algorithms, Birth of Computer Science: Early Computers and Turing Machines, Birth of Information Technology: Claude Shannon and Shannon Entropy, Introduction to Graph Theory and Network Science, Topologies and the Graph Isomorphism Problem, Network prototypes: Small World, scale-free, modular and bipartite networks, Network properties: local cohesiveness, global reach, Cliquishness, Link Density, Preferential attachment of nodes, Hubs. ( 6 hrs )

3. BiC3. Biomolecules and their interplay

   Macro-molecules of life and their structural units in brief: Nucleotides and Nucleic Acids, Amino acids and Proteins, Carbohydrates and Polysaccharides, Anionic and Zwitterionic lipids, Introduction to gene and protein sequences, Genomes and Proteomes, Open Reading Frames, Introns - Exons - Cistrons, The central dogma of Molecular Biology, Mutations: synonymous and non-synonymous replacements, silent, neutral, in-dels, gene duplication, Conserved and Variable parts of a gene and its impact on a gene-product, Coding and Non-coding parts of the genome. Impact of non-coding part on gene expression and regulation, Introduction to Epigenetics and chromatin biology, post translational modifications. ( 6 hrs )

4. BiC4. Sequence analysis

   Brief description of sequencing techniques for nucleic acids and proteins, The Sanger (chain termination) method, the ninhydrin method, Polymerase Chain Reaction (PCR), Multiple Sequence Alignments (MSA), Local (Needleman-Wunsch) and Global (Smith-Watermaan) Alignments, Scoring matrices: PAM and BLOSUM, BLAST, e-value, iterative (psi-BLAST), Molecular Evolution and Phylogeny, Homologs, Orthologs and Paralogs, Human Genome Project, Next generation sequencing. ( 6 hrs )

5. BiC5. Learning and Intelligence in advanced computing

   Computational Complexity, Hard Problems, Combinatorial Optimizations, the Graph Coloring Problem, Heuristics and greedy algorithms, Monte Carlo and Genetic Algorithms, Machine Learning and Artificial Intelligence, Regression and Classification, Neural Networks (NN), Random Forrest Classifiers (RCF), Support Vector Regressions (SVM), Idea of interpretable machine learning for the future, Proposition of Personalized medicines. ( 6 hrs )

6. BiC6. Biomoleular structural dynamics

   Introduction to Biomolecular Structure and Dynamics, eigenvalues and eigenvectors, Bond lengths, Bond Angles and Torsion Angles, Internal, Local and global Frames of References, Molecular Superposition, Transformations Matrices, Translation and Rotations, Normal Modes, Brief recapitulation of experimental structure determination methods: X-ray Crystallography, cryo-Electron Microscopy, SAXS, NMR. ( 6 hrs )

7. BiC7. Amino acids and Proteins

   Amino Acid Biochemistry and Protein Structure, Primary, Secondary, Tertiary, Quaternary associations, Backbone dihedrals and the Ramachandran Plot, Conformational Variation and the Dunbrack’s Rotamer Library, Protein Domains, Multi-domain Proteins, Evolution of protein functions, Structural Classification of Proteins (SCOP), Protein taxonomy: Class, family, super-family, fold, Helix bundles and beta barrels, Structural highlight of classic protein examples: Hemoglobin, Cyclophilin, Immunoglobulins, Collagen and the triple helix. ( 6 hrs )

8. BiC8. Probing Biomolecular Interactions

   Biomolecular Recognition and Molecular Docking, Docking Algorithms, Blind and Guided docking, Receptor and Ligand, Active and allosteric sites, Deep pockets and Grooves, Binding modes, Scoring of Docked poses: Quality Estimates and Scoring Functions, Z-score, Mentioning of CAPRI: the Protein Olympic for Critical Assessment of PRediction of Interaction, Shape and electrostatic complementarity, the Complementarity Plot, Solvent Accessibility and burial, statistical potentials, semi-empirical pseudo energy functions. ( 6 hrs )

9. BiC9. Computations and coding

   Computer Architectures, Shell and Kernel, Operating Systems, DOS, Unix, Linux, Microsoft, Mac, basic shell commands and their combined use, shell scripting (.csh, .bash), Introduction to Programming, Procedural programming and C, Object Oriented Programming and C++, String handling in PERL, number crunching in FORTRAN 90, Minimalistic syntax and Python, Interactive programming and Haskell, Plotting and curve drawing in MATLAB, Octave. ( 6 hrs )

10. BiC10. Basic Programming exercises in Bioinformatics.

    Handling FASTA Sequences and coordinate (PDB) files. Identifying recurring motifs a sequence(s), transcribing the complementary strand from a given sequence, translating a given ORF into a protein sequence, Computing main-chain bond lengths, bond angles and torsion angles in proteins, constructing the Ramachandran Plot. Translating and Rotating a molecular object, Third and Forth Atom Fixations. ( 6 hrs )

Optional Sections (select two out of four choices):

1. BiO1. Macromoleuclar Folding and Structure prediction.

   The Protein Folding Problem, Anfenson’s thermodynamic hypothesis, Second Genetic Code, Protein Structure Prediction, physics-based, knowledge-based and hybrid approaches, Co-evolutionary approaches, Deep learning and alpha folds, Hydrophobic collapse and hydrophobic cores, the Fold Recognition problem, conservation in structures (folds) vs. sequences, decoys, threading and cross-threading, side-chain prediction and SCWRL, twilight and midnight zones of protein sequence alignment. Mentioning of CASP: the Protein Olympic for Critical Assessment of Structure Prediction. Brief mentioning of RNA structure prediction. ( 6 hrs )

2. BiO2. Macromoleuclar Packing and electrostatics

   Protein packing: jigsaw puzzle, nuts and bolts, oil drop models, packing density and Voronoi polyhedra, packing motif in contrast to secondary structural motifs, point and surface contact networks in proteins, protein electrostatics: continuum and explicit models, Recapitulation of Coulomb's law, Poisson-Boltzmann Method, distance dependent dielectric, DelPhi - Gaussian and multi-dielectric advents, consideration of local pKa, the Inverse protein folding problem: Introduction to protein design, Design of alternatively packed hydrophobic cores, design of novel functionalities in proteins, design targeted at the globular - disorder interface. ( 6 hrs )

3. BiO3. Intrinsic Disorder in Proteins

   IDPs and IDPRs, anti-thesis of the ‘one sequence? one structure? one function’ paradigm in proteins, The globular - disorder interface, disorder - to - order transitioning ‘protean’ residues, Loops and structural flexibility, Transient Salt-bridge dynamics and electrostatics in sustaining protein disorder, structural degeneracy and self-organized criticality, Self-aggregation and amyloid formation, Biomedical relevance, Fold switch proteins, Membrane proteins, Stability, strength and weaknesses of amino acid residues across globular and membrane proteins, Membrane embedding, Drugging of membrane proteins. ( 6 hrs )

4. BiO4. Introduction to Molecular Dynamic (MD) simulations

   Recapitulation of Newton’s Laws of Motion, Relationship between Force and Potentials, Force-fields: Predominant force-fields at the macro- and micro-scopic dimensions, Bonding and Non-bonding potentials, Periodic Boundary Conditions, Solvation, Restraints and Constraints, Harmonic constraints, Energy minimization - zero Kelvin structure; Leap-Frog algorithm, Replica Exchange MD simulation; Umbrella Sampling; Time scales of MD simulations - from early days to current state-of-the-art. ( 6 hrs )

Evaluation & Examination

1. Quiz and Problem Solving (part of Continuous Evaluation)

   10 hrs

2. Group wise presentation (~5 groups) of a given Bioinformatic exercise (Topic would be chosen by each group from a collection of theme-topics)(part of Continuous Evaluation)

   10 hrs

3. Written Examination (Theory)

   8 hrs