User:Wayne Decatur/Molecular modeling tools: Difference between revisions
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* [http://www.rosettacommons.org/software/ Rosetta Software Suite] includes Modeling abilities and as a related package, there is [http://pyrosetta.org/ PyRosetta] - an interactive Python-based interface for Interactive Molecular Modeling. | * [http://www.rosettacommons.org/software/ Rosetta Software Suite] includes Modeling abilities and as a related package, there is [http://pyrosetta.org/ PyRosetta] - an interactive Python-based interface for Interactive Molecular Modeling. | ||
* [http://dasher.wustl.edu/tinker/ TINKER] - Software Tools for Molecular Design. | * [http://dasher.wustl.edu/tinker/ TINKER] - Software Tools for Molecular Design. | ||
* [http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] also allows users to calculate comparative models on demand. | |||
* [[PyMOL]] is primarily a molecular viewer but allows some changes to be made. [http://www.pymol.org/news.html Schrödinger took over development of PyMol] after Warren DeLano's unexpected passing on November 3, 2009 | * [[PyMOL]] is primarily a molecular viewer but allows some changes to be made. [http://www.pymol.org/news.html Schrödinger took over development of PyMol] after Warren DeLano's unexpected passing on November 3, 2009 | ||
*[[Swiss-PDBViewer = DeepView]], a powerful and popular free modeling package (not open-source). Has an interface linked to [http://swissmodel.expasy.org/ SWISS-MODEL]. | |||
* YASARA | * YASARA | ||
* UCSF Chimera | * UCSF Chimera | ||
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==See Also== | ==See Also== | ||
* [[Homology model]] | |||
* [[Molecular modeling and visualization software]] | * [[Molecular modeling and visualization software]] | ||
* [http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling List of software for molecular mechanics modeling] at Wikipeida although thoroughness and how current it is are subject to question by the inclusion of RasMol which is simply a viewer with no modeling abilities that has been supplanted by better viewers such as Chime and Jmol not included on the list. | * [http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling List of software for molecular mechanics modeling] at Wikipeida although thoroughness and how current it is are subject to question by the inclusion of RasMol which is simply a viewer with no modeling abilities that has been supplanted by better viewers such as Chime and Jmol not included on the list. | ||
