Monday, January 7, 2013

In the past few months I've dedicated myself to learning about some new or emerging molecular modeling and informatics resources out there that may be taking the place of the standard toolkit.   One area that has remained unchallenged for quite a while is the integrated graphical interface (think SYBYL, Discovery Studio, etc.) that gives you access to a molecular builder, basic molecular modeling tools (MM, MD, etc.) and a diverse array of visualization and analysis tools.  The thing that has remained common about all of the most popular tools is that they are fairly easy to use, cover a reasonably broad array of functionality, and cost lots of money to license.

Is this paradigm finally breaking?  I think so.  Finally there exists a freeware / open source tool that has the look and feel of the commercial interface product:  Avogadro (http://avogadro.openmolecules.net/) produced by OpenMolecules.  It does not yet have much more than a fraction of the functionality of the big commercial products, but it has a wonderful builder that I find more intuitive and efficient than any other tool (albeit with a few minorly clunky aspects here and there), decent visualization and a competent molecular mechanics optimizer.  I find it very useful, but the lack of a molecular dynamics solver is unfortunate.  For those people who need to manipulate and analyze molecules on a budget, though, it's a great find!

1 comment:

  1. Hi, I read your review about molecular editors, it was very helpful, but I have an other question. Can you maybe recommend me a molecule editor, where I can create nice 3D molecules ( like in Avogadro) and also add the written down formula to it on the same page and export it as an illustration? As far as I have understood I can not do that in Avogadro? Do you know a software where this is possible? Thank you in advance!

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