Chlamydia trachomatis is an obligate intracellular human pathogen which can cause trachoma, conjunctivitis, infection of urogenital system and lymphogranuloma-venereum in humans. Preventive measures have recently focused on production of vaccine using the variable domain (VD) extracellular loops of the major outer membrane protein (MOMP). MOMP's crystal structure has not been determined, but serious efforts have been made to propose its structure and function experimentally and theoretically. Our objective is to utilize this information to obtain a consistent secondary and tertiary structure. MOMP functions as general diffusion porin having β-barrel structure. We predict 16 β-stranded transmembrane sheets, and variable domains at proper positions, consistent with available experimental data. Having no sequence similarity of MOMP with other porin proteins, a threading technique was utilized for structure prediction with the outer membrane porin protein (2OMF) of E.Coli as a template. Using hand-threading, MOMP sequence was aligned along the structure of 2OMF. The Modeler program was used to build a final structure (pre-refined). We selected a fragment with five β-sheets and loops containing VD-3 and VD-4. This fragment was further refined (post), using simulations, to get full length β-sheets in a realistic Chlamydial membrane. Our current objective is to continue molecular dynamics (MD) simulations to check the consistency of these (pre- and post-refined) fragments. Implicit water simulations of both refined fragments resulted in loss of secondary and tertiary structure, while MD simulations of post-refined fragment in Chlamydial membrane were stable. This implies that vaccine development requires delivery vehicles that are lipid-like to maintain the stability of these protein fragments. Moreover, future MD simulations of both fragments in a Chlamydial membrane will improve our understanding of stable loop conformations and guide experimentalists in developing a peptide-based vaccine.