User:Wayne Decatur/Molecular modeling tools

(Difference between revisions)

Revision as of 20:03, 22 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.
Modeller
YASARA
UCSF Chimera
Ascalaph Designer
Packmol for molecular dynamic simulations with pdb and xyz files (as described by The Open Science Project)
VMD or Visual Molecular Dynamics is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting and has an extension called MultiSeq, which is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids with a special emphasis is placed on analyzing the data within the framework of evolutionary biology.

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.

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 * UCSF Chimera
 * Ascalaph Designer
-* [http://www.ime.unicamp.br/~martinez/packmol/  Packmol] for molecular dynamic simulations with pdb and xyz files (as described by [http://www.openscience.org/blog/?p=399 The Open Science Project]
+* [http://www.ime.unicamp.br/~martinez/packmol/  Packmol] for molecular dynamic simulations with pdb and xyz files (as described by [http://www.openscience.org/blog/?p=399 The Open Science Project])
+* [http://www.ks.uiuc.edu/Research/vmd/ VMD or Visual Molecular Dynamics] is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting and has an extension called [http://www.scs.illinois.edu/schulten/multiseq/ MultiSeq], which is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids with a special emphasis is placed on analyzing the data within the framework of evolutionary biology.
 ==Related==