To develop a new set of compounds with inhibitory activity against the triosephosphate isomerase of Trypanosoma cruzi (TcTIM), a group of benzimidazole derivatives was studied using four different docking procedures. These docking procedures differ in the number and type of mobile residues considered in the analysis. As a result of this methodology, a clustered analysis of plausible candidate structures was produced. A different set of previously synthesized compounds was used to validate this analysis. The validation showed that the best results correspond to the docking procedure in which the residues near the hydrophobic pocket of the protein's interface were considered mobile. A binding site for the best candidates was identified. Residues Tyr103, Glu105 and Lys113, among others, are important for the binding of this kind of compound. Residue Tyr103 is different in the human TIM, thus establishing a key feature for the future design of selective inhibitors. Copyright © 2011 Elsevier Inc. All rights reserved.