Aim: This study reports structural modeling, molecular dynamics profiling of hypothetical proteins in Chlamydia abortus genome database. Methodology: The hypothetical protein sequences were extracted from C. abortus LLG Genome Database for functional elucidation using in silico methods. Results: Fifty-one proteins with their roles in defense, binding and transporting other biomolecules were unraveled. Forty-five proteins were found to be nonhomologous to proteins present in hosts infected by C. abortus. Of these, 31 proteins were related to virulence. The structural modeling of two proteins, first, WP_006344020.1 (phosphorylase) and second, WP_006344325.1 (chlamydial protease/proteasome-like activity factor) were accomplished. The conserved active sites necessary for the catalytic function were analyzed. Conclusion: The finally concluded proteins are envisioned as possible targets for developing drugs to curtail chlamydial infections, however, and should be validated by molecular biological methods. [GRAPHICS] Lay abstract: Sequencing technologies have generated abundant data on genome and proteins of an organism. The hypothetical proteins are those whose existence is predicted by computational analysis of genes or protein sequences, but practical evidence to prove them are lacking. This study predicts functions of hypothetical proteins in Chlamydia abortus by computational and bioinformatics methods, determining their 3D structures by structural genomics, homology modeling with known proteins and annotating possible catalytic sites. These findings may be helpful for evolving strategies to curtail Chlamydia abortus infection.