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I'm not totally sure which Stack Exchange community this would go in, but Chemistry seemed best. I've been thinking for a long time now, that it would be cool to have a program where you could design your own atomic models, from the sub-atomic scale and up, then test them in a real situation. You could create anything from simple molecular structures to...anything. I've looked around online, but there aren't any programs that you can build your own atomic structure. Anyone know if there are any out there like this?

EDIT: I've tried a few other programs, including Avogadro, this, and another one by PHET.

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  • $\begingroup$ "...your own atomic models..."; do you mean "hypothetical molecules"? $\endgroup$ – M.A.R. Feb 25 '15 at 21:02
  • $\begingroup$ What do you mean by 'hypothetical'? $\endgroup$ – rivermont - Will B. Feb 25 '15 at 21:06
  • $\begingroup$ I mean molecules that don't exist, but since we love logo, we make them up. :) $\endgroup$ – M.A.R. Feb 25 '15 at 21:07
  • $\begingroup$ @MARamezani I mean a program where you could, maybe with a drag & drop interface, create your own models, molecular structures, etc., then put them into a real situation and see how they act. This could maybe be used to create new medicines, simple viruses that could go in and kill a disease, or even new species. Does that help? $\endgroup$ – rivermont - Will B. Feb 25 '15 at 21:19
  • $\begingroup$ William, you might want to have a look at this wikipedia article on docking. $\endgroup$ – Klaus-Dieter Warzecha Feb 25 '15 at 21:22
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You might want to try BioVia's (formerly Accelrys) Discovery Studio Visualizer. This is free software and the "gateway drug" to their sophisticated suite of molecular modeling and chem/bio informatics software. It is a step above the various drawing programs out there and lets the user generate realistic 3-D models of an infinite variety of chemical structures. http://accelrys.com/products/discovery-studio/visualization-download.php

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[…] create your own models, molecular structures, etc., then put them into a real situation and see how they act. This could maybe be used to create new medicines […]

Imagine a huge protein that switches a malfunction (on or off) to be like a lock, while small organic compounds may be seen as possible keys.

You could either

  • synthesize a huge library of potential keys and test them in the lab or
  • build a library of keys on the computer and calculate their geometries, charge distribution, etc. using quantumchemical methods and then again use other programmes to examine the interaction between the keys and the lock.

The latter method, figuring out how good the keys fit, is known as docking.

You might want to have a look at the CADDSuite, developed by Oliver Kohlbacher at the University of Tübingen, but please note that these tools tend to be a tad above the entry level of simple moelcule editors.

For an online service, have a look at SwissDock.

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