Homology Modelling is crucial procedure for structure based drug design when the experimental 3D-structure of the receptor is not available.Modelling of Membrane proteins requires extreme care and presistent validation due to difficulty in obtaining their 3D experimental structures.Although, recently there is increase in the number of crystal strucutre of membrane proteins,many structures having low resolution and high R factors exist in the PDB.However we can improve the accuracy of the model with sequence alignment. This requires manually compiled accurate membrane protein structure datasets.
HOMEP contains homologous membrane proteins dataset which grouped into 11 families of similar topologies accroding SCOP classification except beta-barrels.
These datasets can be used to generate sequence alignments or build models with homologous membrane proteins
Reference:
Forrest L.R., Tang C.L. and Honig B. "On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins" Biophysical Journal 91(2):508-17 2006