Treponematoses (Yaws) is caused by a spirochete bacterium that impacts skin, bones, and joints. It is caused by Treponema pallidum subsp. pertenue, after 9–90 days of infection. It is a disease of poverty, endemic to 15 countries with humid and temperate climate. It was targeted for elimination by the WHO in the 1950s and efforts for this purpose were renewed in 2012. In this study protocol, we outline an informatics method to identify drug target from the core fraction of the sequenced genomes of T. pallidum subsp. pertenue. Phytochemical compounds from traditional Tibetan medicinal plants were then tested in silico against the identified target lipoprotein. Best-docked compound Isorhoeadine (IUPAC name: (1 S ,14 R ,24 S )-24-methoxy-13-methyl-5,7,19,21,25-pentaoxa-13-azahexacyclo[12.11.0.02,10.04,8.015,23.018,22]pentacosa-2,4(8),9,15(23),16,18(22)-hexaene) from Meconopsis horridula was further analyzed for interaction and binding energy changes via dynamics simulation. This protocol can be utilized for identifying phytochemical inhibitors from traditional medicines from other geographical regions or allopathic drug inhibitors against the target protein. It can be extended to other bacterial or pathogenic organisms with sequenced genomes, for finding pan-inhibitors against the species, instead of just targeting a single organism.