Algorithms in Structural Bioinformatics

Integrated approaches on structural bioinformatics. Development and application of geometric algorithms for the modelling and analysis of three dimensional macromolecular structures. Genome and proteins- primary, secondary and tertiary macromolecular structures. Macromolecular databases (e.g. Protein Data Bank), experimental data from X-ray crystallography and NMR. Sequences, comparison and alignment, alignment with gaps. Dynamic programming, complexity. Determination of secondary structure. Tertiary structure and folding: distance geometry, Conformation space and conformation search. Similarities and matching of macromolecular structures, in silico docking of bioactive molecules (ligands) to protein receptors: molecular surfaces (α-shapes, Connolly surface). Geometric data structures, geometric search, geometric hashing.