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1. Molecular Operating Environment Installations

• Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology.
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Molecular Operating Environment Installations

Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and MAC OS X. Main application areas in MOE include structure-based design,^[1]fragment-based design,^[2]pharmacophore discovery, medicinal chemistry applications, biologics applications, protein and antibody modeling, molecular modeling and simulations, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.

References[edit]

1. ^Reynolds CH, Merz KM, Ringe D, eds. (2010). Drug Design: Structure- and Ligand-Based Approaches (1 ed.). Cambridge, UK: Cambridge University Press. ISBN978-0521887236.
2. ^Erlanson DA, McDowell RS, O'Brien T (July 2004). 'Fragment-based drug discovery'. J. Med. Chem. 47 (14): 3463–82. doi:10.1021/jm040031v. PMID15214773.

External links[edit]

Jmol is computer software for molecular modellingchemical structures in 3-dimensions.^[2] Jmol returns a 3D representation of a molecule that may be used as a teaching tool,^[3] or for research e.g., in chemistry and biochemistry.It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna.

A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways.For example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc.^[4]Jmol supports a wide range of chemical file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML). There is also a JavaScript-only (HTML5) version, JSmol, that can be used on computers with no Java.^[5]

The Jmol applet, among other abilities, offers an alternative to the Chime plug-in,^[3] which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol requires Java installation and operates on a wide variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, and Safari.

Screenshots[edit]

• Crystal structure of an H/ACA box RNP from Pyrococcus furiosus.

• Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right).

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• A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of DNA.

• Eubacterial 70S Ribosome from Thermus thermophilus.

See also[edit]

• Chemistry Development Kit (CDK)

References[edit]

1. ^Jmol translations
2. ^Chen, Jim X. (2008), Springer (ed.), Guide to Graphics Software Tools, p. 471, ISBN978-1-84800-900-4
3. ^ ^abHerráez, A (2006), 'Biomolecules in the Computer: Jmol to the Rescue', Biochemistry and Molecular Biology Education, 34 (4): 7, doi:10.1002/bmb.2006.494034042644
4. ^Herráez, A (2007), Lulu (ed.), How to Use Jmol to Study and Present Molecular Structures, Volume 1, p. 21, ISBN978-1-84799-259-8
5. ^'JSmol'. Retrieved 2015-11-02.

External links[edit]

• Official website
  • Wiki with listings of websites, wikis, and moodles
• Willighagen, Egon; Howard, Miguel (June 2007). 'Fast and Scriptable Molecular Graphics in Web Browsers without Java3D'. doi:10.1038/npre.2007.50.1.