Approximate Point Set Match for Partial Protein Structure Alignments

We present a practical algorithm and its implementation which is able to find partial and approximative matches of patterns, such as small parts of molecules, in large search spaces, such as complete proteins. The search pattern can be matched in a flexible way including torsion of parts of the pattern. The alignment of the pattern in the search space can be based on distance functions other than RMSD. Being a general method for the approximate point set match problem, the algorithm can be applied to other fields of pattern recognition.