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Introduction to structural biology; primary, secondary and tertiary structure. Dynamic programming and complexity; sequences and alignment, alignment with gaps. Structure comparison and alignment. Databases of biological information (e.g. Protein Data Bank), experimental data from Nuclear Magnetic Resonance and X-ray crystallography. Study and computation of 3D structure, conformational search. Distance geometry, triangular and tetrangle inequality, distance matrix. Molecule kinematics and rigid transformations; degrees of freedom. Solving of polynomial systems via linear algebra. Molecular surface modeling and flexibility; Delaunay triangulation, alpha-shapes. Applications to protein docking. Geometric data structures and geometric hashing.
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