The PANM Database (Protostome DB) was constructed for the first in the year 2015. The aim of the construction was to provide a public platform for researchers to efficiently annotate the next-generation sequencing (NGS) data arising out of genome sequencing projects of species belonging to Arthropoda, Mollusca, and Nematoda (Protostome group). The web-based interface has paramount importance in improving the process of sequencing data with a greater number of noteworthy hits. In the subsequent year, we released an update to the database (PANM-DB v1.0) that contained twice the number of protein sequences (7,571,246) as compared to the original database and the inclusion of Cephalopod sequences. We now release the third database update (PANM-DB v3) with the incorporation of 11,615,243 protein sequences. The size of PANM-DB v3 is smaller, only 6% of NCBI nr database, and significantly reduces the NGS data annotation time. Like the previous versions of the database, PANM-DB v3 is freely downloadable from http://panm.sch.ac.kr/ for local BLAST analysis.