Molecular visualization
From Bioinformatics.Org Wiki
Contents |
Software
Easy to use
The following visualization packages have extensive built-in help, and do not require that you learn any command language. All of these work in web browsers online.
- Proteopedia.Org - the easiest and most powerful[1] way to communicate 3D structure-function relationships online. It is a wiki that incorporates the Jmol applet (see below) for 3D interactive viewing. Molecular scenes can be imbedded in articles, and rotated and zoomed with the mouse. Generating new, custom molecular scenes is very easy using the built-in Scene Authoring Tools -- all menus, buttons, and forms. Molecular scenes are linked to the adjacent text describing them with green links.
- FirstGlance in Jmol (firstglance.jmol.org) - a free, open-source user-interface to Jmol utilized in the 3D View links in papers in the journal Nature that report new macromolecular structures. FirstGlance in Jmol is probably the easiest-to-use[1] dedicated 3D macromolecular structure visualization software. It provides mostly "canned" views that reveal major structural features, but does not, for the most part, allow generation of customized molecular views. It is particularly strong in making it easy to visualize the noncovalent interactions between any moiety and the remainder of the structure. For more on its ease of use, and a comparison with other packages, see What Is FirstGlance in Jmol?.
- Polyview-3D (polyview.cchmc.org/polyview3d.html) - the easiest place to create publication-quality custom molecular views. It also creates high-quality animations suitable for Powerpoint® slides. Polyview-3D generates its images with PyMOL (see below).
- Protein Explorer (proteinexplorer.org) - an extensive and powerful open-source user-interface to the free MDL Chime browser plugin (see below) that enables users to create rotatable, zoomable customized molecular views. It is very easy to use, although taking full advantage of it requires many hours of experience because its power inevitably leads to some complexity. Protein Explorer has more help for beginners in macromolecular structure than do Proteopedia.Org or FirstGlance in Jmol. Because it depends on Chime, its use is now limited to MS Windows computers. Nevertheless, in 2009, there is no other package[1] that combines the ease of use with the power of Protein Explorer.
- Friend (ilyinlab.org/friend) - Integrated Front-End application for multiple structure visualization and multiple sequence alignment. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.
More powerful, more complicated to use
Effective use of these packages requires learning some more complicated controls and/or command language. In return, they have considerably more power.
- SPADE (sites.google.com/view/spade) - the Structural Proteomics Application Development Environment. SPADE provides community tools for development and deployment of essential structure and sequence equipment. Includes a chemical probing suite to support experimental verification of predicted structural models. Written in Python with scripting tools available. Runs on Linux, Windows and Mac.
- Jmol (jmol.org) - a free, open-source java-based program available in stand-alone or applet forms. It uses a superset of the RasMol/Chime command language. It is widely accepted as a replacement for Chime. The Jmol applet is used in the Proteopedia.Org wiki. Jmol is extremely powerful both for small molecules (e.g. molecular orbitals) and macromolecules (e.g. symmetry operations, unit cells, crystal contacts, translucent surfaces and cavities, arbitrary objects, animations, etc. etc.).
- BALLView ([1]) - a powerful open-source molecular modeling and visualization tool. It is available for Windows, MacOS X and Windows. BALLView provides powerful visualization capabilities for proteins, nucleic acids and small molecules. The modeling functionality includes various molecular mechanics methods (molecular dynamics, geometry optimization) using
various force fields (AMBER, CHARMM, MMFF94). The functionality of BALLView can be extended and scripted through a convenient Python interface.
- PyMol - a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. PyMOL is extremely powerful and is very popular with crystallographers. A large percentage of macromolecular structure figures in scientific journal articles are made with PyMOL. Although it is open source, use of PyMOL requires a modest subscription fee, except for educational use.
- RasMol - a free, open-source stand-alone program first released in 1993, remains very popular. The program and reference manual are available from rasmol.org.
- MDL Chime (www.mdl.com) - a free browser plugin released in 1996. It was the best tool for free, web-browser based visualization from 1996 until about 2004, when it was superceded by Jmol (see above). It is not open-source, and development effectively ceased before 2000. Although hundreds of tutorials and other resources remain available only in Chime in 2009, Chime is now largely of historical interest.
- Friend (ilyinlab.org/friend) - a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases. Friend is also now availabe in Applet form, which empowers users with all the functionality currently found in Friend, and provides a new web-based presentation platform, with detailed organization and manipulation of structure/sequence information, at the press of a button.
Additional
- Chimera - excellent molecular graphics package with support for a wide range of operations, including flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, docking
- Garlic - a free molecular visualization program
- Ghemical - a molecular modelling package; graphical user interface is built on GTK2; both quantum-mechanical and forcefield-based methods are supported, and it is also possible to add new methods
- Oslet - a molecular modeling and simulation environment in Java, mainly for education
- Spock - a full-featured molecular graphics program
- VEGA - developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc.
- VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
- UGENE - visual suite allowing visualization of PDB and MMDB proteins
See also
Notes
- ↑ 1.0 1.1 1.2 Opinion of Eric Martz, who authored FirstGlance in Jmol and Protein Explorer, and is a member of the Proteopedia.Org development team.
External links
- Top Five Macromolecular Visualization Resources for the rest of us
- Molecular modeling and visualization software at Proteopedia.Org
- Extensive lists of free and commercial visualization and modeling software at the World Index of Molecular Visualization Resources, molvisindex.org
