Structure Motif Discovery and Mining the PDB

We describe an algorithm for the automatic discovery of recurring patterns in protein structures. The patterns consist of individual residues having a defined order along the protein's backbone that come close together in the structure and whose spatial conformations are similar. The residues in a pattern need not be close in the protein's sequence. The work described in this paper builds on an earlier reported algorithm for motif discovery. This paper describes a significant improvement of the algorithm which makes it very efficient. The improved efficiency allows us to use it for doing unsupervised learning of patterns occurring in small subsets in a large set of structures, a non-redundant subset of the PDB database of all known protein structures.

• Type: Conference
• Year: 2000
• Where: GCB
• Authors: Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor
• Keywords: Algorithm, Biometrics, Earlier Reported Algorithm, GCB 2000, Protein Structures