Seminar in Structural Bioinformatics

A protein is one of the fundamental molecules in the living cell. Proteins have different functions; they can provide structure (ligaments, fingernails, hair), help in digestion (stomach enzymes), aid in movement (muscles), and play a part in our ability to see (the lens of our eyes is pure crytalline protein) .  A protein is a long chain of amino acids, that can be viewed as a 1D string over a 20 letter alphabet. However, they perform  their tasks as 3D molecules, and their structure affects their functionality. While "conventional" bioinformatics treats molecules as 1D objects, structural bionformatics looks at their 3D structure. Although  protein structure is determined by it's 1D sequence, structure prediction problem (also known as the folding problem) is still unsolved. There are experimental techniques for solving protein structures (X-ray Crystallography and NMR). The increasing number of solved structures (more then 24,000)  requires efficient algorithms for structure comparison (are the given molecules similar? what is the similarity?), docking (is there an interaction between two input molecules? What is the structure of their complex?)  and more.  The seminar lectures will deal with these problems.

Examples of proteins 3D structures: (from  http://www.rcsb.org/pdb/molecules/molecule_list.html)