CycloMolder software: building theoretical cyclodextrin derivatives models and evaluating their host:guest interactions

摘要

This paper presents a software to build theoretical models of cyclodextrin derivatives and evaluate their host:guest interactions, using a graphical user interface in an intuitive way. This goal was outlined to facilitate the studies of molecular modeling, particularly from experimental groups with demands in this research field. The software (CycloMolder) consists of two modules: CycloGen and CycloDock. The first module builds theoretical models with more than one chemical structure to represent a cyclodextrin derivative. These structures are divided into configurations and conformations. The configurations can be homologous structures, with different molar substitution ratio, or just positional isomers. Conformers are generated from the built configurations. The second module performs the docking calculations between the host (cyclodextrins and/or their derivatives) and guest molecules, using the AutoDock Vina program, and displays the final results of the modeled inclusion complexes, including graphs showing the distribution energy and intermolecular interactions present in the host:guest complex.