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The biological activity of pharmaceutical compounds is often based on
controlling certain reactions in complex metabolic processes of the human
organism. Therefore developing small organic molecules (ligands) that strongly
bind to a special protein molecule (receptor) is an important problem. The
binding process is also called molecular docking. The forces dominating the
docking process are weak short-range interactions that require the molecules
to fit both geometrically and chemically. To predict the strength of binding
and the three-dimensional structure of potential ligands in the complex of
ligand and receptor is one of the central questions in the development of
new drugs (rational drug design).
Three dimensional structures of receptor molecules are only available in some
cases. Therefore, we have two kinds of problems: the
Docking Problem (receptor structure is known) and the
Superposition Problem (receptor structure is not known).
The RELIWE project aims at developing efficient algorithms and data structures
for the docking and superposition problems and their implementation in the
software tools called FlexX and FlexS respectively.
