Hi..I am trying to model two proteins (Plasmodium reticulocyte-binding protein homologue 4 and 5). From Literature review, I have found out that the protein "Py235 of P.yoelii" (http://www.rcsb.org/pdb/explore/explore.do?structureId=3HGF) is the closest there is to finding a template theoretically.

Attached are the alignments that have been generated by MODELLER, and visually I could detect so many gaps.

From the tutorials in the MODELLER website, i saw tutorial number 4 "Difficult Modeling. Model a sequence based on a low identity to a template" that employs the use of mGenThreader.

Is this the best option? Please assist.

Regards....kevinkariuki