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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 | + | * [http://chemagic.com/web_molecules/script_page_large.aspx The ISU CheMagic USM O=CHem Virtual Molecular Model Kit], as detailed [http://chemagic.com/chemsketch/ 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 [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. * 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://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]. | ||
Revision as of 16:16, 3 September 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.
- 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
- 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.
