Local structural alignment is an effective method to detect the local similarities between two protein structures. Orengo & Taylor (1993) have already developed a local structural alignment method by using a double dynamic programming algorithm. In the method, the similarity between a pair of residues is evaluated as the similarity between the pair of the structural environments corresponding to the residues. However, it is difficult to evaluate the structural similarities between a pair of proteins related by circular permutation, because the structural environment of a residue drastically differs from that of the corresponding residue of the circularly permuted protein. In this manuscript, we propose a new method to construct a structural environment that is robust against circular permutation. We examined its efficiency in the detection of the local structural similarity by the reconstructed structural environments.

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The Receptor Database (RDB, http://impact.nihs.go.jp/RDB.html) has been developed to help researchers retrieve various data related to receptors in a systematic manner. The system has been available on the Internet for public use since 1997. Recently, the RDB contents were updated and its links expanded to other Web sites and supplemented with additional database modules. The new RDB aims to support structural biologists and drug designers not only for the examination of receptor-ligand binding but also for the elucidation of post binding signal transduction pathways.

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Data on genetic polymorphisms particularly single nucleotide polymorphisms (SNPs) are now being rapidly accumulated and put on the Internet for public use. It is time consuming and cumbersome, however, for general researchers who are interested in certain groups of genes or proteins to collect and update genetic variation data for these genes and proteins. An agent system is developed to search for and fetch SNPs data related to those genes and proteins pre-registered in the system. The system is tested and improved for collecting SNPs of different types of proteins, including certain drug target proteins.

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