The toxin Lasiotoxin-2 (LpTX2) is a 49aa residue peptide is isolated from the venom of Lasiodora parahybana. In this assay we have predicted the binding affinity of toxin Lasiotoxin-2 (LpTX2) having 49 amino acids, which shows 41 nonamers. Peptide fragments of the neurotoxin can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in neurotoxin studies. Small segment ‘11-KEGKPCKPKGCKCNDKDNKDHKKCS-36’ of toxin protein called the antigenic epitopes is sufficient for eliciting the desired immune response. Immunization cassettes should be capable of immunizing of broad immunity against both humoral and cellular epitope thus giving vaccines the maximum ability to deal with neurotoxin protein of Opisthacanthus madagascariensis. Binding ability prediction of antigen peptides to MHC class molecules is important in vaccine development, We also found the SVM based MHCII-IAb peptide regions,26- DKDNKDHKK, 27- KDNKDHKKC, 8-CDIKKEGKP, 5- TLECDIKKE, (optimal score is 0.557); MHCII-IAd peptide regions, 32-HKKCSGGWR, 9- DIKKEGKPC, 20- KGCKCNDKD, 35- CSGGWRCKL, (optimal score is0.363);MHCII-IAg7 peptide regions, 13-EGKPCKPKG, 3- ECTLECDIK ,37- GGWRCKLKL, 22- CKCNDKDNK, (optimal score is 0.988); and MHCII- RT1.B peptide regions, 1- FFECTLECD, 5-TLECDIKKE, 22- CKCNDKDNK, 40- RCKLKLCLK, (optimal score is 0.556) which represented predicted binders from neurotoxin protein. We have predicted a successful immunization.