List of molecular graphics systems
From Wikipedia, the free encyclopedia
 |
This article may require cleanup to meet Wikipedia's quality standards. (Consider using more specific cleanup instructions.) Please help improve this article if you can. The talk page may contain suggestions. (September 2009) |
This is a list of software systems that are used for visualizing macromolecules [1].
The tables below indicates which types of data can be visualized in each system: EM = Electron microscopy; HM = Homology modelling; MD = Molecular Dynamics; MM = Molecular modelling and molecular orbital visualization; MRI = Magnetic resonance imaging; NA = Nucleic Acids; NMR = nuclear magnetic resonance; Optical = Optical microscopy; SMI = Small molecule interactions; XRC = X-ray crystallography data such as electron density.
Contents |
[edit] Stand-alone systems
| Name | Data | License | Technology | Citation | Comments | |
|---|---|---|---|---|---|---|
| Ascalaph Graphics | MM MD | free | C++ | [2] | ||
| Avizo | EM MM MRI Optical XRC | commercial | Windows, Linux, Mac | [3] | ||
| Avogadro | MM XRC MD | free and open-source | C++/Qt, can be extended with Python modules | |||
| BALLView | MM Nucleic Acids XRC SMI | free and open-source, GPL | C++ and Python; Windows, Linux, Solaris, and MacOS X | BALL project | BALLView uses OpenGL and the real time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes. | |
| Cn3D | free | stand-alone application | [6][7] | |||
| CheVi | SMI | free | stand-alone application | |||
| chemkit | MM MD | free and open-source | C++ | Software library for cheminformatics, molecular modelling and visualization. | ||
| Coot | free | [8] | ||||
| Crystal Studio | MM XRC | commercial | Windows | [9] | Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns | |
| CueMol | MM XRC | free and open-source | Windows, MacOS X, and Linux application based on OpenGL and Mozilla XULRunner. | |||
| Friend | MM SA MSA | free | Win, Linux | [10][11] | Fast, can work with hundreds of structures and thousands of sequences; millions of atoms. Crosstalk between sequence and structure modules. Sequence module based on Jalview. Accurate Structural alignment by TOPOFIT method. Also available as applet to interface sequence/structure databases. | |
| Gabedit | XRC MM | free and open-source | C | [12] | ||
| g0penMol | MD MM | free | [13] | |||
| ICM-Browser | free | Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery | [14] | multiple objects, symmerty, 3D wavefront, alignments, chemistry, tables, plots | ||
| Jmol | free and open-source | Java applet or stand-alone application | [15] | Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry | ||
| MDL Chime | free for noncommercial use, proprietary | C++ browser plugin for Windows only | [16] | Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol. | ||
| Molden | MM XRC | [17] | ||||
| MOE | MM XRC | commercial | Molecular Operating Environment (MOE) | |||
| Molekel | MM XRC | free and open-source | Java3D applet or stand-alone application | [citation needed] | ||
| NOCH | free and open-source | [18] | ||||
| O | free for noncommercial use | [19] | see also [1] | |||
| Procreate | free | C# stand-alone application | [20] | Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects | ||
| PyMOL | XRC SMI EM | free for noncommercial use, open-source | Python | [21] | According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.[citation needed] | |
| Qmol | MM | free, open-source | C | [22] | Provided by DNASTAR | |
| RasMol | free and open-source | C stand-alone application | [23][24][25] | |||
| Sirius | free and open-source | Java3D applet or stand-alone application | ||||
| SPARTAN | MM QM | commercial | stand-alone application | [26] | visualize and edit biomolecules, extract bound ligands from PDB files for further computational analysis, full molecular mechanics and quantum chemical calculations package with streamlined graphical user interface. | |
| SRS3D Viewer | HM | free and open-source | Java3D applet or stand-alone application | [27][28] | Integrates 3D structures with sequence and feature data (domains, SNPs, etc.). | |
| UCSF Chimera | XRC SMI EM MD | free for noncommercial use | Python | [29][30] | Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[31] | |
| VMD | EM MD MM | free for noncommercial use | C++ | [32][33] | ||
| WebMol | free | Java applet and stand-alone | [34][35] | Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations. | ||
| WHAT IF | HM XRC | shareware for academics | stand-alone | [36] | Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup. | |
| Yasara | HM NMR XRC | commercial; free version for education and elementary structure work | stand-alone | [37] | Very advanced graphics; Best in homology model optimisation in CASP-2008; many drug design options; |
[edit] Web-based systems
| Name | Data | License | Technology | Citation | Comments |
|---|---|---|---|---|---|
| Relibase | SMI | partly free (full functionality requires a license) | Java applet integrated into web front-end | [38] | |
| WebMol | free | Java applet and stand-alone | [34][35] | Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations. | |
| SRS3D Viewer | HMSMI | free and open-source | Java3D applet or stand-alone application | [27][28] | Integrates 3D structures with sequence and feature data (domains, SNPs, etc.). |
| Proteopedia | HMSMI | free | Java applet integrated into web front-end | Integrates 3D structures and different views on those with text descriptions of the structures |
[edit] See also
- Biological data visualization
- List of Open Source Bioinformatics software
- List of software for molecular mechanics modeling
- List of nucleic acid simulation software
- List of microscopy visualization systems
- Molecular graphics
- Software for protein structure visualization
[edit] References
- ^ O'Donoghue, SI; Goodsell, DS; AS, Frangakis; F, Jossinet; Laskowski, M; Nilges, E; Saibil, HR; Schafferhans, A et al (2010). "Visualization of macromolecular structures". Nature methods 7 (3 Suppl): S42–55. doi:10.1038/nmeth.1427. PMID 20195256.
- ^ "Ascalaph Graphics". http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html. Retrieved 24 September 2009.[self-published source?]
- ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". http://www.avizo3d.com. Retrieved August 5, 2010.[self-published source?]
- ^ "Avizo Official Users' Forum". http://www.mc3dviz.com/avizo-forum/. Retrieved August 5, 2010.[self-published source?]
- ^ "Avizo - Examples of applications (movies)". http://www.youtube.com/user/Avizo3D. Retrieved August 5, 2010.[self-published source?]
- ^ Wang, Y; Geer, LY; Chappey, C; Kans, JA; Bryant, SH (2000). "Cn3D: sequence and structure views for Entrez". Trends in biochemical sciences 25 (6): 300–2. doi:10.1016/S0968-0004(00)01561-9. PMID 10838572.
- ^ "Cn3D Home Page". http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml. Retrieved 28 November 2011.
- ^ Emsley, P; Cowtan, K (2004). "Coot: model-building tools for molecular graphics". Acta crystallographica D 60 (Pt 12 Pt 1): 2126–32. doi:10.1107/S0907444904019158. PMID 15572765.
- ^ "Crystal Studio". http://www.crystalsoftcorp.com/. Retrieved 24 September 2009.[self-published source?]
- ^ Abyzov, A; Errami, M; Leslin, CM; Ilyin, Valentin (2005). "Friend, an integrated analytical front-end application for bioinformatics". Bioinformatics 18 (21): 3677–8. doi:10.1093/bioinformatics/bti602. PMID 16076889.
- ^ "Friend - An Integrated front-end Application for Bioinformatics". http://ilyinlab.org/friend. Retrieved 24 September 2005.[self-published source?]
- ^ "Gabedit A graphical user interface for computational chemistry packages". http://gabedit.sourceforge.net.
- ^ "g0penMol". http://www.csc.fi/english/pages/g0penMol. Retrieved 24 September 2009.[self-published source?]
- ^ http://www.molsoft.com/icm_browser.html
- ^ "Jmol: an open-source Java viewer for chemical structures in 3D". http://www.jmol.org. Retrieved 24 September 2009.[self-published source?]
- ^ "Chime Pro". Symx. http://www.symyx.com/products/software/cheminformatics/chime-pro/index.jsp. Retrieved 24 September 2009.[self-published source?]
- ^ "MOLDEN a visualization program of molecular and electronic structure". http://www.cmbi.ru.nl/molden/molden.html.
- ^ "NOC Homepage". http://noch.sourceforge.net/. Retrieved 24 September 2009.[self-published source?]
- ^ "O 12 Release Notes". http://xray.bmc.uu.se/alwyn/Distribution/ov11_12/ov12.html. Retrieved 24 September 2009.[self-published source?]
- ^ "Home Page for Procreate". http://members.iinet.net.au/~lahg/procreate/. Retrieved 21 March 2011.[self-published source?]
- ^ "PyMOL Molecular Viewer - Home Page". http://www.pymol.org. Retrieved 24 September 2009.[self-published source?]
- ^ "QMOL". http://www.dnastar.com/qmol/. Retrieved 24 September 2009.[self-published source?]
- ^ Sayle, RA; Milner-White, EJ (1995). "RASMOL: biomolecular graphics for all". Trends in biochemical sciences 20 (9): 374. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.
- ^ Bernstein, HJ (2000). "Recent changes to RasMol, recombining the variants". Trends in biochemical sciences 25 (9): 453–5. doi:10.1016/S0968-0004(00)01606-6. PMID 10973060.
- ^ "Home Page for RasMol and OpenRasMol". http://www.rasmol.org/. Retrieved 24 September 2009.[self-published source?]
- ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
- ^ a b O'donoghue, SI; Meyer, JE; Schafferhans, A; Fries, K (2004). "The SRS 3D module: integrating structures, sequences and features". Bioinformatics (Oxford, England) 20 (15): 2476–8. doi:10.1093/bioinformatics/bth260. PMID 15087318.
- ^ a b "General information about SRS 3D". http://srs3d.org/About/. Retrieved 24 September 2009.[self-published source?]
- ^ Pettersen, EF; Goddard, TD; Huang, CC; Couch, GS; Greenblatt, DM; Meng, EC; Ferrin, TE (2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of computational chemistry 25 (13): 1605–12. doi:10.1002/jcc.20084. PMID 15264254.
- ^ "UCSF Chimera". http://www.cgl.ucsf.edu/chimera. Retrieved 24 September 2009.[self-published source?]
- ^ Meng, EC; Pettersen, EF; Couch, GS; Huang, CC; Ferrin, TE (2006). "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics 7: 339. doi:10.1186/1471-2105-7-339. PMC 1570152. PMID 16836757. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1570152.
- ^ Humphrey, W; Dalke, A; Schulten, K (1996). "VMD: visual molecular dynamics". Journal of molecular graphics 14 (1): 33–8, 27–8. doi:10.1016/0263-7855(96)00018-5. PMID 8744570.
- ^ "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd. Retrieved 24 September 2009.[self-published source?]
- ^ a b Walther, D (1997). "WebMol--a Java-based PDB viewer". Trends in biochemical sciences 22 (7): 274–5. doi:10.1016/S0968-0004(97)89047-0. PMID 9255071.
- ^ a b "WebMol Java PDB Viewer". http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl. Retrieved 24 September 2009.[unreliable source?]
- ^ "WHAT IF homepage". http://swift.cmbi.ru.nl/whatif. Retrieved 24 September 2009.[self-published source?]
- ^ "YASARA - Yet Another Scientific Artificial Reality Application". http://www.yasara.org. Retrieved 24 September 2009.[self-published source?]
- ^ Hendlich, M (1998). "Databases for protein-ligand complexes". Acta crystallographica. Section D, Biological crystallography 54 (Pt 6 Pt 1): 1178–82. doi:10.1107/S0907444998007124. PMID 10089494.
[edit] External links
- Saric, Marc. "Free Molecular Modelling Programs". http://www.marcsaric.de/index.php/Free_Molecular_Modelling_Programs. A rather detailed, objective, and technical assessment of about 20 tools.
- "PDB list of molecular graphics tools". http://www.rcsb.org/pdb/static.do?p=software/software_links/molecular_graphics.html.
- "World Index of Molecular Visualization Resources". http://www.molvisindex.org.
- "Molecular Visualization Resources by Eric Martz". http://molviz.org.
