Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the
African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm
[Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible
for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII)
and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The
objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular
modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of
National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology
modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was
performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation
(RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII
and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The
EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures
predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures
are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is
essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.