Various amino acids play a role in formation of continuous organic framework, hydroxyapatite crystal formation, mineral nucleation, orientation of mineral crystallites. Self-assembling peptides have shown to diffuse into the porosities in the enamel, attract calcium and allow its saturation. Aim: Aim of this study was to design peptides and identify potential amino acids for enamel remineralization. Methodology: Glutamine, Aspartic acid, Phosphorylated Serine were the amino acids identified for the analysis. The influence of the positions of these amino acids at the N terminal and C terminal were assessed. 6 peptides were designed for computational analysis. Designing of peptide and receptor of amelogenin was done using Chemdraw Ultra Ver, Binding affinity was analysedin HPEPDOCK tool. Toxicity was analysed using ToxinPred and Peptide Ranker Analysis. Peptide P11-4 was the positive control. Results: Positive control of P114 showed the highest binding affinity score of -419.327 Kcal/mol when compared with other peptides. Peptide 3 (-294.701 Kcal/mol), 4 (-294.668 Kcal/mol), and 6 (-293.411 Kcal/mol) showed the least binding affinity score. But a nearly equivalent binding affinity score compared to P114 peptide was obtained in the Peptide 1 (-327.112 Kcal/mol), 2 (-310.596 Kcal/mol) and 5 (-328.708 Kcal/mol). All the peptides showed non-toxic condition, while the peptide 2 (0.251) and peptide 5 (0.244) showed better bioavailability. Conclusion: Newly designed peptides were stable. Binding affinity was comparable to P 11- 4. The designed peptides were non-toxic. Aspartic acid had binding affinity closer to P 11-4 and biocompatibility more than P 11-4.