Abstract: Background: Mitotic kinesin Eg5, a member of the kinesin superfamily, plays an essential role in cell proliferation while the regulated cell proliferation is essential for survival, but uncontrolled cell proliferation increases the risk of cancer. Therefore development of new efficient Eg5 inhibitors is very important in cancer chemotherapy. S-trityl-L-cysteine (STLC) and their analogues are known as potent allosteric inhibitors for Eg5. In the present work, we try to develop some 3D-QSAR techniques including CoMFA and COMSIA methods to modeling and prediction of the Eg5 inhibitory activities for new STLC analogues. The result of this study not only can use to predict the Eg5 inhibitory activities of untested chemicals but also to design more active chemicals.