Physics:List of molecular graphics systems

From HandWiki
Short description: none

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

Name Data License Technology Citations Comments
Amira EM MM MRI Optical SMI XRD Proprietary[2] Windows, Linux, Mac [3][self-published source?] Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ [4][self-published source?] Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRD Proprietary[5] Windows, Linux, Mac [6][self-published source?] Avizo is derived from Amira and focusing on materials science.
Avogadro MM XRD MD Free open-source, GPL C++, Qt, extensible via Python modules
BALL Molecular dynamics MM NMR LGPL open-source Standalone program [7]
Cn3D Free open-source Standalone program [8] In the NCBI C++ toolkit
Coot XRD Free open-source
Gabedit XRD MM Free open-source C [9]
Jmol Free open-source Java (applet or standalone program)
Transpiled HTML5/JavaScript for browser 		[10][self-published source?] 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 [11][self-published source?] Build and visualize molecule and periodic systems (crystal, structures, fluids...), animate trajectories, visualize molecular orbitals, density, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors.
Mol* MM MD NA SMI XRD Free open-source (MIT) TypeScript (WebGL, React) [12] Viewer currently used by RCSB-PDB and EMBL/PDBe. Contains a scripting language.
Molden MM XRD Proprietary, free use academic [13]
Molecular Operating Environment (MOE) HM MD MM NA QM SMI XRD 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 XRD Free open-source Java 3D applet or standalone program
PyMOL MM XRD SMI EM Open-source[14] Python [15][self-published source?] According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.[citation needed]
RasMol Free open-source C standalone program [16][17][18][self-published source?]
SAMSON MM MD SMI MRI Proprietary, limited free version Windows, Linux, Mac. C++ (Qt) [19] Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Sirius Free open-source Java 3D applet or standalone program No longer supported as of 2011.
Scigress MM QM Proprietary[20] Standalone program [21] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary[22] Standalone program [23] 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 XRD SMI EM MD Free open-source[24] for noncommercial use[25] Python [26][27][self-published source?] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[28]
VMD EM MD MM Free open-source for noncommercial use[29] C++ [30][31][self-published source?]
WHAT IF HM XRD Proprietary, shareware for academics Fortran, C, OpenGL, standalone [32][self-published source?] 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 [33][self-published source?] Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Key

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


See also

References

  1. ↑ "Visualization of macromolecular structures". Nature Methods 7 (3 Suppl): S42-55. March 2010. doi:10.1038/nmeth.1427. PMID 20195256. 
  2. ↑ Amira commercial license
  3. ↑ "Amira for Life & Biomedical Sciences". 2019-02-28. http://www.amira.com. 
  4. ↑ "Ascalaph". http://www.biomolecular-modeling.com/Products.html. 
  5. ↑ Avizo commercial license
  6. ↑ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. http://www.avizo3d.com. 
  7. ↑ Hildebrandt, Andreas (25 October 2010). "BALL - biochemical algorithms library 1.3.". BMC Bioinformatics 11: 531. doi:10.1186/1471-2105-11-531. PMID 20973958. 
  8. ↑ "Cn3D: sequence and structure views for Entrez". Trends in Biochemical Sciences 25 (6): 300–2. June 2000. doi:10.1016/S0968-0004(00)01561-9. PMID 10838572. 
  9. ↑ "Gabedit A graphical user interface for computational chemistry packages". http://gabedit.sourceforge.net. 
  10. ↑ "Jmol: an open-source Java viewer for chemical structures in 3D". http://www.jmol.org. 
  11. ↑ "Chime Pro". Symx. http://www.symyx.com/products/software/cheminformatics/chime-pro/index.jsp. 
  12. ↑ Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodová, Radka; Berka, Karel; Bazgier, Václav; Velankar, Sameer; Burley, Stephen K et al. (2 July 2021). "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures". Nucleic Acids Research 49 (W1): W431–W437. doi:10.1093/nar/gkab314. PMID 33956157. 
  13. ↑ "Molden a visualization program of molecular and electronic structure". http://www.cmbi.ru.nl/molden/molden.html. 
  14. ↑ "PyMOL License". Jan 8, 2010. https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE. 
  15. ↑ "PyMOL Molecular Viewer". http://www.pymol.org. 
  16. ↑ "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences 20 (9): 374–376. September 1995. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707. 
  17. ↑ "Recent changes to RasMol, recombining the variants". Trends in Biochemical Sciences 25 (9): 453–5. September 2000. doi:10.1016/S0968-0004(00)01606-6. PMID 10973060. 
  18. ↑ "Home Page for RasMol and OpenRasMol". http://www.rasmol.org/. 
  19. ↑ SAMSON Connect
  20. ↑ Scigress commercial license
  21. ↑ "Scigress". fqs.pl. 12 September 2014. http://www.fqs.pl/Chemistry_Materials_Life_Science/products/scigress. 
  22. ↑ Spartan webpage
  23. ↑ Spartan Tutorial & User's Guide ISBN:1-890661-38-4
  24. ↑ "UCSF Chimera code repository". https://www.rbvi.ucsf.edu/trac/chimera/browser/trunk. 
  25. ↑ UCSF Chimera license
  26. ↑ "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry 25 (13): 1605–12. October 2004. doi:10.1002/jcc.20084. PMID 15264254. 
  27. ↑ "UCSF Chimera". http://www.cgl.ucsf.edu/chimera. 
  28. ↑ "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics 7: 339. July 2006. doi:10.1186/1471-2105-7-339. PMID 16836757. 
  29. ↑ Visual Molecular Dynamics license
  30. ↑ "VMD: visual molecular dynamics". Journal of Molecular Graphics 14 (1): 33–8, 27–8. February 1996. doi:10.1016/0263-7855(96)00018-5. PMID 8744570. 
  31. ↑ "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd. 
  32. ↑ "WHAT IF homepage". http://swift.cmbi.ru.nl/whatif. 
  33. ↑ "YASARA – Yet Another Scientific Artificial Reality Application". http://www.yasara.org. 

External links



Retrieved from "https://handwiki.org/wiki/index.php?title=Physics:List_of_molecular_graphics_systems&oldid=3282426"