List of molecular graphics systems

This is a list of notable software systems that are used for visualizing macromolecules.[1]

The tables below indicate which types of data can be visualized in each system:

Standalone systems
Name Data License Technology Citations Comments
Amira EM MM MRI Optical SMI XRC Proprietary[2] Windows, Linux, Mac [3] Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ [4] Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRC Proprietary[5] Windows, Linux, Mac [6] Avizo is derived from Amira and focusing on materials science.
Avogadro MM XRC MD Free open-source, GPL C++, Qt, extensible via Python modules
Cn3D Free open-source Standalone program [7] In the NCBI C++ toolkit
Gabedit XRC MM Free open-source C [8]
Jmol Free open-source Java applet or standalone program [9] Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime Proprietary, free use noncommercial C++ browser plugin for Windows only [10] Build and visualize molecule and periodic systems (crystal, structures, fluids...), animate trajectories, visualize molecular orbitals, denity, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors.
Molden MM XRC Proprietary, free use academic [11]
Molecular Operating Environment (MOE) HM MD MM NA QM SMI XRC Proprietary Windows, Linux, OS X; SVL programming language Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications.
Molekel MM XRC Free open-source Java 3D applet or standalone program
PyMOL XRC SMI EM open-source, Python Python [12] According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.
RasMol Free open-source C standalone program [13][14][15]
SAMSON MM MD SMI MRI Free Windows, Linux, Mac. C++ (Qt) [16] Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Sirius Free open-source Java 3D applet or standalone program
Scigress MM QM Proprietary[17] Standalone program [18] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary[19] Standalone program [20] 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.
UCSF Chimera XRC SMI EM MD Proprietary, free use noncommercial[21] Python [22][23] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[24]
VMD EM MD MM Proprietary, free use noncommercial[25] C++ [26][27]
WHAT IF HM XRC Proprietary, shareware for academics Fortran, C, OpenGL, standalone [28] 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 Proprietary, limited free version C-assembly, Windows, Linux, Mac [29] Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Web-based systems
Name Data License Technology Citations Comments
EzMol MM Proprietary, free to use JavaScript, WebGL, 3Dmol.js [30] Built on top of the 3dmol.js viewer, this tool uses a wizard-style interface.

See also

References
  1. O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. (March 2010). "Visualization of macromolecular structures". Nature Methods. 7 (3 Suppl): S42-55. doi:10.1038/nmeth.1427. PMC 7097155. PMID 20195256.
  2. Amira commercial license
  3. "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.
  4. "Ascalaph". Retrieved 24 September 2009.
  5. Avizo commercial license
  6. "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.
  7. Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (June 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.
  8. "Gabedit A graphical user interface for computational chemistry packages".
  9. "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.
  10. "Chime Pro". Symx. Retrieved 24 September 2009.
  11. "Molden a visualization program of molecular and electronic structure".
  12. "PyMOL Molecular Viewer". Retrieved 24 September 2009.
  13. Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.
  14. Bernstein HJ (September 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.
  15. "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009.
  16. SAMSON Connect
  17. Scigress commercial license
  18. "Scigress". fqs.pl. 12 September 2014.
  19. Spartan webpage
  20. Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  21. UCSF Chimera license
  22. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218.
  23. "UCSF Chimera". Retrieved 24 September 2009.
  24. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE (July 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.
  25. Visual Molecular Dynamics license
  26. Humphrey W, Dalke A, Schulten K (February 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.
  27. "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009.
  28. "WHAT IF homepage". Retrieved 24 September 2009.
  29. "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.
  30. Reynolds CR, Islam SA, Sternberg MJ (July 2018). "EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures". Journal of Molecular Biology. 430 (15): 2244–2248. doi:10.1016/j.jmb.2018.01.013. hdl:10044/1/56880. PMC 5961936. PMID 29391170.
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