PDB-by-RMSD: The New Service and Tool for Searching Protein Structures

Modern databases and search engines for structural biology are very sophisticated and versatile. Ho wever, scientific life discovers new research topics almost every day. For instance scientific visualizat ion is a field where distances between different conformations play a crucial ro le. In our research of protein motions we have faced a problem of searching of structures with known Root Mean Square Dev iation (RMSD). In spite of the fact that there is a set of tools giving possibility of search on different databases, it is impossible to set RMSD interval between NM R models of some protein as the search criterion. PDB-by-RM SD is a tool, developed to provide such possibility. It can be used in protein motion researching or protein visualization(1-5).

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