User:Wayne Decatur/Molecular modeling tools
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* [http://www.symyx.com/micro/jdraw/ 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. | * [http://www.symyx.com/micro/jdraw/ 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. | ||
* [http://chemagic.com/chemsketch/ CheMagic and the Jmol Virtual Molecular Model Kit] Jmol & JME enabling users to generate molecular models; user generated Jmol models can also be created using [http://www.acdlabs.com/products/draw_nom/ ACD/Labs’ ChemSketch]. | * [http://chemagic.com/chemsketch/ CheMagic and the Jmol Virtual Molecular Model Kit] Jmol & JME enabling users to generate molecular models; user generated Jmol models can also be created using [http://www.acdlabs.com/products/draw_nom/ ACD/Labs’ ChemSketch]. | ||
| - | * [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=146 Jmol on its own now has some ability to be directly used as a chemistry modeling kit] for small molecules and there is a [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=147 responsive docking ability for moving/sculpting small molecules relative to large molecules] in the works. | + | * [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=146 Jmol on its own now has some ability to be directly used as a chemistry modeling kit] for small molecules and there is a [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=147 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 [http://chemapps.stolaf.edu/jmol/docs/examples-11/jsdraw/jstest.htm here]. |
* http://www.chemaxon.com/products/marvin/ ChemAxon's Marvin Sketch] and [http://www.chemdoodle.com/ ChemDoodle] has the ability to draw reactions and structures. And you can put chemistry on the web with [http://metamolecular.com/software Metamolecular's ChemWriter]. | * http://www.chemaxon.com/products/marvin/ ChemAxon's Marvin Sketch] and [http://www.chemdoodle.com/ ChemDoodle] has the ability to draw reactions and structures. And you can put chemistry on the web with [http://metamolecular.com/software Metamolecular's ChemWriter]. | ||
==See Also== | ==See Also== | ||
[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 17:00, 15 July 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.
- 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
- 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.
- CheMagic and the Jmol Virtual Molecular Model Kit Jmol & JME 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
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.
