The transcription factor termed activating transcription factor 1 (ATF1) is a member of the large bZIP superfamily of transcription factors which is categorized by a basic DNA binding domain and a leucine zipper domain. ATF1 binds to cyclic-AMP response elements (CRE); however its role is not well defined. Studies have shown that over expression of ATF1 has been correlated with the neoplastic phenotype of lymphoma and the continuous proliferation of lymphocyte. More recent studies have also shown ATF1 to have a role in the tumor growth of human melanoma. An antibody, Mab41.4, has been produced that disrupts the interactions of ATF1 to CRE DNA. Molecular modeling techniques were employed to investigate the mechanism of interaction between ATF1 and its inhibitory antibody. Conformational Memories (CM), a conformational search method that uses both simulated annealing and Monte Carlo methods to efficiently and completely explore the conformational space of a target molecule or peptide, was employed to elucidate the structure of the epitope sequence from ATF1. MMC, a simulation program that uses a fragment driven approach to identify likely binding sites on a given target, was then utilized to locate the most probable binding sites for the epitope.