List of molecular graphics systems

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

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]

[4] [5]
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
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.
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;

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

See also

References

  1. ^ 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. 
  2. ^ "Ascalaph Graphics". http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html. Retrieved 24 September 2009. 
  3. ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". http://www.avizo3d.com. Retrieved August 5, 2010. 
  4. ^ "Avizo Official Users' Forum". http://www.mc3dviz.com/avizo-forum/. Retrieved August 5, 2010. 
  5. ^ "Avizo - Examples of applications (movies)". http://www.youtube.com/user/Avizo3D. Retrieved August 5, 2010. 
  6. ^ 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. 
  7. ^ "Cn3D Home Page". http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml. Retrieved 28 November 2011. 
  8. ^ 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. 
  9. ^ "Crystal Studio". http://www.crystalsoftcorp.com/. Retrieved 24 September 2009. 
  10. ^ 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. 
  11. ^ "Friend - An Integrated front-end Application for Bioinformatics". http://ilyinlab.org/friend. Retrieved 24 September 2005. 
  12. ^ "Gabedit A graphical user interface for computational chemistry packages". http://gabedit.sourceforge.net. 
  13. ^ "g0penMol". http://www.csc.fi/english/pages/g0penMol. Retrieved 24 September 2009. 
  14. ^ http://www.molsoft.com/icm_browser.html
  15. ^ "Jmol: an open-source Java viewer for chemical structures in 3D". http://www.jmol.org. Retrieved 24 September 2009. 
  16. ^ "Chime Pro". Symx. http://www.symyx.com/products/software/cheminformatics/chime-pro/index.jsp. Retrieved 24 September 2009. 
  17. ^ "MOLDEN a visualization program of molecular and electronic structure". http://www.cmbi.ru.nl/molden/molden.html. 
  18. ^ "NOC Homepage". http://noch.sourceforge.net/. Retrieved 24 September 2009. 
  19. ^ "O 12 Release Notes". http://xray.bmc.uu.se/alwyn/Distribution/ov11_12/ov12.html. Retrieved 24 September 2009. 
  20. ^ "Home Page for Procreate". http://members.iinet.net.au/~lahg/procreate/. Retrieved 21 March 2011. 
  21. ^ "PyMOL Molecular Viewer - Home Page". http://www.pymol.org. Retrieved 24 September 2009. 
  22. ^ "QMOL". http://www.dnastar.com/qmol/. Retrieved 24 September 2009. 
  23. ^ 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. 
  24. ^ 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. 
  25. ^ "Home Page for RasMol and OpenRasMol". http://www.rasmol.org/. Retrieved 24 September 2009. 
  26. ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  27. ^ 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. 
  28. ^ a b "General information about SRS 3D". http://srs3d.org/About/. Retrieved 24 September 2009. 
  29. ^ 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. 
  30. ^ "UCSF Chimera". http://www.cgl.ucsf.edu/chimera. Retrieved 24 September 2009. 
  31. ^ 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. 
  32. ^ 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. 
  33. ^ "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd. Retrieved 24 September 2009. 
  34. ^ 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. 
  35. ^ a b "WebMol Java PDB Viewer". http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl. Retrieved 24 September 2009. 
  36. ^ "WHAT IF homepage". http://swift.cmbi.ru.nl/whatif. Retrieved 24 September 2009. 
  37. ^ "YASARA - Yet Another Scientific Artificial Reality Application". http://www.yasara.org. Retrieved 24 September 2009. 
  38. ^ 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. 

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