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Plant oils are very important for domestic and industrial use. Biodiesel can be obtained from plant seed oil. Biodiesel is currently popular and in demand due to the high cost of petroleum and to avoid pollution. It is time to increase plant seed oil production and conduct research to find ways of enhancing its production. We studied two species of oil seed plants, i.e. Ricinus communis and Glycine max, with varying amounts of oil content. Proteins from six categories of enzymes involved in fatty acid biosynthesis were selected for study. The 3D structures were predicted using different structure prediction tools. The structures were validated and selected on the basis of quality factors. The pairs of proteins were compared by pairwise sequence alignment using Clustal W and structural superposition by Chimera Matchmaker. The physiochemical properties were studied by PROTPARAM. In R. communis, eighteen structures were selected from I Tasser, thirteen from Swiss Model, and two from Raptorx. In G. max, twenty structures were selected from I Tasser, nine from Swiss Model, and four from Raptorx. The highest percent identity in pairwise sequence alignment was observed between the two species for biotin carboxylase. Biotin carrier was least identical between these two species. Monogalactosyldiacylglycerol desaturase (FAD5) showed the highest percentage of structural identity between the two species while ER phosphatidate phosphate was least identical. Eight proteins in both species had an instability index below 40. Eight proteins in R. communis and five in G. max were acidic in nature. Fourteen proteins in R. communis and seventeen in G. max were hydrophobic. The aliphatic index of all proteins was above 50 with which conferes good thermal stability. [ABSTRACT FROM AUTHOR]