The antibody M alpha2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin alpha, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin alpha:M alpha2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy, was docked to models of the variable fragment of the antibody combining site by using a method based on surface complementarity and maximization of buried surface area while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3.