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It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era. Two molecules are said to be similar if the RMSD (root mean square deviation) of the two molecules is less than or equal to some given constant bound. In this paper, we consider an important, fundamental problem of finding all the similar substructures from 3-D structure databases of chain molecules (such as proteins), with considerationdoi:10.1186/1748-7188-5-7 pmid:20047663 pmcid:PMC2830924 fatcat:vdudzahft5htjmvvnfn4zxhrby