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Structural Bioinformatics
Proteins: Principles of protein structure; physico-chemical properties, anatomy of proteins– Hierarchical organization of protein structure - Primary. Secondary, Supersecondary, Tertiary and quaternary structure; Molecular forces (Covalent & non-covalent); Ramachandran Map, protein folding (Chaperones and Chaperonins); DNA & RNA: structure & types of DNA double helices A,B,Z; geometrical & structural features; DNA-Protein interactions, t-RNA tertiary structure, databases of structure of protein, nucleotide & other small molecules.
Secondary structure: Basic principles on which the prediction methods of first, second and third generation are based; algorithms of Chou Fasman, GOR methods; PHD, PSI-PRED methods; concepts in measuring the accuracy of predictions (Q3, Segment overlap, Mathew’s correlation coefficient etc.); t-RNA structure prediction. Homology Modeling, Fold recognition or threading, Ab initio methods; automated methods.
Protein structure comparison and classification: classes, folds (SCOP, CATH); the concepts in 3D structure omparison, purpose of structure comparison, algorithms such as FSSP, VAST and DALI; Protein-protein interactions databases such as DIP, PPI server and tools for analysis of protein-protein interactions,
Molecular Mechanics Based: Introduction to Molecular and Quantum Mechanics, Concepts of force fields, Potential Energy Functions; Molecular fitting; Energy Minimisation (Non-derivative and derivative methods);Conformational searches, Geometry optimization algorithms: Steepest descents, conjugate gradient; Description of Forcefield such as MM3, Dreiding, AMBER, CHARMM etc.
Newton's equations for many particles, Verlet algorithms, Types of dynamics simulations: adiabatic, constant T, annealed, etc., Conformational searching using MD and other methods, Free energy calculations, Dynamics of Bio-macromolecules; Application of Molecular Simulation.
1. Creighton T. E. “Protein Structure: A Practical approach”. Oxford ; Washington, DC : IRL Press 1989. 2. Sternberg M.J.E. “Protein Structure Prediction: A practical approach”. Oxford University Press, 1996. 3. Branden, Carl & Tooze, John. “Introduction to Protein Structure” Garland Publishing, 1991. 4. Structural Bioinformatics - Methods of biochemical Analysis V. 44 Philip E. Bourne (Editor), Helge Weissig (Editor) New Jersey. Wiley-Liss, 2003.
1. Hill, H.A.O., Sadler, P.J. & Thomson, A.J. “Metal sites in proteins and models”. Berlin. Springer, 1999. 2. Creighton T. “Protein Folding”. W. H. Freeman & Co., New York, 1992. 3. “Computational methods for protein folding : advances in chemical physics’’ vol. 120 by Friesner, R.A. Ed., Prigogine, L. Ed. & Rice, S.A.New York. John wiley & sons, Inc. publication, 2002. 4. Andrew Leach. “Molecular Modeling: Principles and Applications”. Prentice Hall, 2001. 5. Fasman, G.D. “Prediction of protein structure and the Principles of protein conformation”. New York. Plenum Press, 1989.
