MedeA Docking Create Host-Guest and Surface-Guest Models


MedeA ®[1] Docking automatically creates, adjusts, and refines host-guest and surface-guest systems. Employing the well-known Metropolis Monte Carlo algorithm [2], MedeA Docking evaluates van der Waals interactions to generate and assess stable system configurations. The resulting host-guest structures may then be employed in forcefield and first-principles based simulations. MedeA Docking can be invoked interactively within the MedeA Environment or by using MedeA Flowcharts on the JobServer. MedeA Docking is a building tool that allows you to combine systems automatically to create the starting points for further simulation studies.

Key Benefits

  • Saves time through accelerated and automated model construction and refinement
  • Simplifies automated Flowchart based model construction for screening, allowing construction of host-guest and surface-guest systems without interactive manipulation
  • Explores multiple guest configurations, searching and evaluating many possible binding configurations

Alcohol molecules docked in a microporous material using MedeA Docking.

Key Features

  • Automatic combination of host and guest structures
  • Minimization of steric overlap between host and guest
  • Automated energy based refinement of sorbate position and orientation
  • Interactive screen updates, and full user control of model view and scale during docking
  • Control of simulation length, Monte Carlo temperature, maximum position, and rotation displacements
  • Combination of multiple sorbates with host structure
  • Employs Metropolis Monte Carlo Algorithm, allowing user control of the employed search (via control of acceptance probability within the temperature setting)
  • For use with surface, microporous, and porous materials models

‘I will say that enzyme and glucoside must fit together like lock and key in order to be able to exercise a chemical action on each other’

Emil Fischer, 1852-1919

Required Modules

  • MedeA Environment
  • MedeA JobServer and MedeA TaskServer

Find Out More

To learn more about the use of docking to provide insights into host-guest interactions in materials science, see the following papers on the following topics:

  • General host-guest interactions [3],
  • Understanding templating with organic additives [4],
  • Simulating CFC interactions [5], and host-guest
  • Interactions in isomerization [6].

Watch this webinar to learn more about atomistic simulation using the MedeA Environment:

[1]MedeA and Materials Design are registered trademarks of Materials Design, Inc.
[2]N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, E. Teller, “Equations of State Calculations by Fast Computing Machines”, J. Chem. Phys. 21, 1087 (1953)
[3]C.R.A. Catlow, J.M. Thomas, C.M. Freeman, P.W. Wright, R.G. Bell, “Simulating and predicting crystal structures”, Proc. R. Soc. Lond. A 442, 85 (1993)
[4]D.W. Lewis, C.M. Freeman, C.R.A. Catlow, “Predicting the templating ability of organic additives for the synthesis of microporous materials”, J. Phys. Chem. 99, 11194 (1995)
[5]A.R. George, C.M. Freeman, C.R.A. Catlow, “A computational investigation of zeolite-chlorofluorocarbon interactions” Zeolites 17, 466 (1996)
[6]P.T. Tschaufeser, C.M. Freeman, “Computer simulation studies of the selectivity of zeolites for different butene isomers” Catal Lett. 60, 77 (1999)