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

  • Marcelo Montenegro RabelloEmail author
  • Larissa Araújo Rolim
  • Pedro José Rolim Neto
  • Marcelo Zaldini Hernandes
Original Article


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.


Cyclomolder Cyclodextrin Inclusion complex Molecular modeling Molecular docking 



This study was funded by the Foundation to Support Science and Technology in the State of Pernambuco, Brazil (Grant Number APQ-0278-4.03/16); and National Council for Scientific and Technological Development, Brazil (Grant Number 300070/2018-7).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Central of Analysis of Drugs, Medicines and FoodFederal University of San Francisco ValleyPetrolinaBrazil
  2. 2.Department of Pharmaceutical SciencesFederal University of PernambucoRecifeBrazil

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