Special issue paper PAR-3D-BLAST: A parallel tool for searching and aligning protein structures present a parallel tool, parallel 3D-BLAST (PAR-  3D-BLAST), which lists the similar structures to the query protein. Each protein in the result list has a  structural similarity score and an alignment to the query structure. The presented tool is implemented to fit  both the standalone multi-core computers and clusters of multi-core nodes. The achieved speedup is linear  and scalable.