Abstract

Introduction In this chapter we discuss the application of novel pattern matching methods to the biomolecular recognition and docking problem. The problem of receptor-ligand recognition and binding is encountered in a very large number of biological processes. For example, it is a prerequisite in cell-cell recognition and in enzyme catalysis and inhibition. The type of molecules involved is very diverse as well: proteins, nucleic acids (DNA and RNA), carbohydrates and lipids. Whereas the receptor molecules are usually large (often proteins), the ligands can be fairly large (e.g. proteins) or small, such as drugs or cofactors. Efficient docking algorithms of drug molecules to target receptor proteins is one of the major ingredients in a computer assisted drug design scheme. The docking task usually requires shape complementarity of the participating molecules. This complementarity reflects the effect of the van der Waals interactions, which are very sharp at short distances. T

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