Protein structure comparison is a vital process in several tasks like the prediction of protein structures and functions and detecting the proteins evolutionary relationships. The expansion of both the parallel computational hardware and the discovered protein structures stimulates the growth of the parallel computational tools to handle this massive data of proteome. Here, we 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. The experimental results outline that the speedup increases as the size of the database increases. Using a cluster of 35 computing cores, the tool constructs the database of the entire structural classification of proteins dataset, 108,116 protein entries, in less than 6min and with average query time of 1.45s. The obtained speed up is 20 times for database construction and 17 times for searching the query. The tool is an open source and free to use, distribute, and share; it is available at http://aca.hnu.cn/par3dblast. Copyright © 2013 John Wiley & Sons, Ltd.