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User:Wayne Decatur/Molecular modeling tools
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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. | ||
Revision as of 16:08, 12 October 2010
- Schrödinger Molecular Modeling Platform - Small Molecule and Macromolecule Modeling and Simulations.
- Accelrys Discovery Studio - Accelrys and Symyx merged effective July 1, 2010.
- Rosetta Software Suite includes Modeling abilities and as a related package, there is PyRosetta - an interactive Python-based interface for Interactive Molecular Modeling.
- TINKER - Software Tools for Molecular Design.
- 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. 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 SWISS-MODEL.
- YASARA
- UCSF Chimera
- Ascalaph Designer
- Packmol for molecular dynamic simulations with pdb and xyz files (as described by The Open Science Project
Related
- Symyx JDraw Applet - as they describe it: "In addition to accessing the no-fee Symyx Draw desktop application, students, teachers, and researchers working in a non-commercial setting can now access capabilities for rapidly drawing chemical structures and chemically intelligent queries in Web applications–capabilities built on industry-leading Symyx chemistry representation technology." Symyx Draw is similar to ISIS/Draw and has advanced features.
- The ISU CheMagic USM O=CHem Virtual Molecular Model Kit, as detailed here, uses CheMagic and the Jmol Virtual Molecular Model Kit & JME Molecular Editor enabling users to generate molecular models; user generated Jmol models can also be created using ACD/Labs’ ChemSketch.
- Jmol on its own now has some ability to be directly used as a chemistry modeling kit for small molecules and there is a responsive docking ability for moving/sculpting small molecules relative to large molecules in the works. * Similarly, using Jmol that can now read SMILES format, it was possible to connect Jmol to Chemene's JSDraw that will output SMILES to JMol for rendering, see the demo here.
- http://www.chemaxon.com/products/marvin/ ChemAxon's Marvin Sketch] and ChemDoodle has the ability to draw reactions and structures. And you can put chemistry on the web with Metamolecular's ChemWriter.
See Also
- Homology model
- Molecular modeling and visualization software
- 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.
