List of molecular graphics systems

This is a list of 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
Ascalaph Designer MM MD QM Proprietary C++ [2] Graphics, model building, molecular mechanics, quantum chemistry.
Athena/Zeus XRC MM Proprietary, free use noncommercial Delphi, Java, Solaris, SPARC, Windows, Linux Athena is derived from the larger Zeus project.
Avizo EM MM MRI Optical XRC Proprietary[3] Windows, Linux, Mac [4]
Avogadro MM XRC MD Free open-source, GPL C++, Qt, extensible via Python modules
BALLView MM NA XRC SMI Free open-source, GPL C++, Python; Windows, Linux, Solaris, Mac OS X Uses OpenGL and the real-time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualizing in several different modes.
CAVER Analyst MD EM XRC Proprietary, free use noncommercial Java; Windows, Linux, Solaris, Mac OS X Protein tunnel analysis software that delivers fast results for protein engineers and structural biologists. Combines CAVER algorithm with advanced visualizing methods in easy to use software to speed results.
CCP4mg XRC MM NA SMI Free open-source C++, Python, OpenGL, Windows, OS X, Linux Primarily for crystallographers. Structure analysis. Publication quality images and movies.
ChemDoodle 3D MM Proprietary Java, OpenGL, Windows, macOS, Linux User interface for creating advanced and customizable scientific graphics. Build and interact with molecules using a real time dynamic physical modeling simulation. Visualize small molecules, proteins, nucleic acids and periodic structures.
Cn3D Free open-source Standalone program [5] In the NCBI C++ toolkit
CheVi SMI Free open-source Standalone program
chemkit MM MD Free open-source C++ Software library for cheminformatics, molecular modelling and visualization.
chemlab MM MD Free open-source, GPL Python Extensible viewer written in Python and OpenGL. It includes a framework and an API to work with chemical data.
Coot XRC MM NA SMI EM Free open-source C++, Python, Scheme, GTK+, OpenGL, Windows, OS X, Linux [6] Designed mostly for protein and protein-ligand structure modeling via X-ray data.
Crystal Studio MM XRC Proprietary[7] Windows Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
Crystals Free open-source Windows Single crystal X-ray structure refinement and analysis.
CueMol MM XRC Free open-source Windows, OS X, Linux, OpenGL and XULRunner
Deneb MD MM Proprietary, trial version available Linux, Windows Graphical user interface and builders for relevant calculation packages: SIESTA, VASP, QE, etc.
Dino EM MD MM XRC Free open-source Linux, OS X Supports 5 data-types: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans), geom (geometric primitives such as lines). Last updated in 2009.
DRAWxtl Free open-source Linux, openVMS, OS X, Windows
Friend MM SA MSA Free open-source Win, Linux [8] Crosstalk between sequence and structure modules. Sequence module based on Jalview. Accurate Structural alignment by TOPOFIT method. Also available as applet.
GDIS Free open-source C [9] Display, manipulate, and analyze isolated molecules and periodic structures.
Gabedit XRC MM Free open-source C [10]
gOpenMol MD MM Free open-source Development finished years ago, no support available (as it's outdated). The program is available for download, including source code.
GPView QM MD Proprietary, free use academic C++ Display molecule structures, orbitals and densities, and MD trajectories. Calculate MO, NO, NTO, NDO, densities: total SCF, gradient norm, Laplacian, hole-particle, detachment-attachment, transition.
HyperChem HM MM QM MD NA NMR SMI XRC Proprietary Windows
ICM-Browser Free open source Windows, Mac, Linux, C++ [11] Multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots. Plugin and activeICM for Web delivery.
Jmol Free open-source Java applet or standalone program [12] Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
Maestro HM MM MD SMI XRC Proprietary, free use academic[13] C++, Qt, Python API [14]
MAPS MM QM MD SMI XRC Optical Proprietary C++, Python API [15] Build and visualize molecular and periodic systems (crystal, surface, interfaces, amorphous systems…), extensive property visualization and calculations capabilities (3D-grid, spectra...).
MDL Chime Proprietary, free use noncommercial C++ browser plugin for Windows only [16] 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 [17]
Molgif Free open-source Go An easy-to-use tool to create GIF animations of molecules
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
MView MM XRC MD Free open-source C++, Python, GTK+; Linux
O Proprietary, free use noncommercial [18] see also
OpenStructure EM HM MD MM XRC Free open-source Linux, OS X, Windows [19] Computational Structural Biology Framework in C++ and Python, aimed at users and developers, high-end visualization of atomic structures, electron densities and molecular trajectories.
ORTEP-III Free open-source Fortran Ball-and-stick type illustrations
Procreate Proprietary C# standalone program [20] Currently views SEQ and PDB files. Programmed in pure managed .NET via advanced DirectX rendering and effects
PyMOL XRC SMI EM Free open-source, Python Python [21] According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.
Qmol MM Free open-source C [22] Provided by DNASTAR
RasMol Free open-source C standalone program [23][24][25]
SAMSON MM MD SMI Free Windows, Linux, Mac. C++ (Qt) [26] 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[27] Standalone program [28] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary[29] Standalone program [30] 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.
Tapering lines FMG, MAE, SDF, MOL Proprietary, free use for academic purposes Standalone program Use it in Stereochemistry. Visualize enantiomers or relative position of more ring in a compound
UCSF Chimera XRC SMI EM MD Proprietary, free use noncommercial[31] Python [32][33] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[34]
VMD EM MD MM Proprietary, free use noncommercial[35] C++ [36][37]
Vimol MM MD Free open-source C Powerful molecular editor with vim-like interface.
VESTA Free Linux, Mac OS X, Windows Crystal structure visualization and computation
V_Sim Free open-source GTK+; Linux, OS X, Windows Visualizes atomic structures, such as crystals, grain boundaries and more.
WHAT IF HM XRC Proprietary, shareware for academics Fortran, C, OpenGL, standalone [38] Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
XCrySDen Free open-source C, Fortran, Tcl/Tk; Linux, Mac, Windows Crystal and molecule structure visualising
YASARA HM NMR XRC Proprietary, limited free version C-assembly, Windows, Linux, Mac [39] 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
3Dmol Free open-source JavaScript, WebGL Object-oriented JavaScript library for visualizing molecular data.
Aquaria HM SMI Free open-source Java 3D applet or standalone program Integrates 3D structures with sequence and feature data: domains, SNPs, etc.
ChemDoodle Web Components Free open-source GPL v3.0 JavaScript, WebGL Derived from the ChemDoodle desktop software, this toolkit allows for the building of scientific visualization software on web and mobile platforms.
EzMol MM Proprietary, free to use JavaScript, WebGL, 3Dmol.js [40] Built on top of the 3dmol.js viewer, this tool uses a wizard-style interface to allow a user to quickly apply some of the most common visualization options to a PDB model.
GLmol MM XRC Free open-source JavaScript, WebGL Early WebGL viewer,[41] not actively developed anymore.
IcmJS Proprietary, free for some uses JavaScript, WebGL A JavaScript/HTML5 version of the ActiveICM plugin, formerly known as ActiveIcmJS.
iCn3D MM Free open-source JavaScript, WebGL Any custom displays and annotations can be reproduced with a URL via Share Link option. STL and VRML files can be exported for 3D printing. Used by NCBI.
JSmol MM XRC HM SMI Free open-source JavaScript and Java Applet Full-featured JavaScript version of Jmol.
LiteMol MM Free open-source TypeScript, WebGL Used by PDBe.
Molmil MM Free open-source JavaScript, WebGL Used by PDBj.
NGL MM Free open-source JavaScript, WebGL [42] Many representations of biomolecules. Used by RCSB PDB.
Prosat+ XRC, NMR Free JavaScript, WebGL, JSMol [43] Display of UniProt features on protein structures possible. Similar structures can be searched.
PV MM Free open-source JavaScript, WebGL Non-photorealistic rendering of ribbons. Used by SwissModel and RCSB PDB.
Relibase SMI Proprietary, part free Java applet [44] Login required to see the website.
Speck Free open-source JavaScript, WebGL Reads only xyz files. Specialized in ambient occlusion.
TRAPP XRC MD Proprietary, free to use JavaScript, WebGL, JSMol [45] Analyses transient pockets on proteins and presents their visualization.
UglyMol XRC Free open-source JavaScript, WebGL Specialized in presenting protein models with electron density maps.

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". Retrieved 24 September 2009.
  3. ↑ Avizo commercial license
  4. ↑ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ Crystal Studio commercial license
  8. ↑ Abyzov, A; Errami, M; Leslin, CM; Ilyin, Valentin (2005). "Friend, an integrated analytical front-end application for bioinformatics". Bioinformatics. 21 (18): 3677–8. doi:10.1093/bioinformatics/bti602. PMID 16076889.
  9. ↑ Fleming, Sean; Rohl, Andrew (2005-01-01). "GDIS: a visualization program for molecular and periodic systems". Zeitschrift für Kristallographie - Crystalline Materials. 220 (5/6). doi:10.1524/zkri.220.5.580.65071. ISSN 2196-7105.
  10. ↑ "Gabedit A graphical user interface for computational chemistry packages".
  11. ↑ "Molsoft L.L.C.: ICM-Browser". molsoft.com.
  12. ↑ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.
  13. ↑ Schrödinger Maestro, free use academic
  14. ↑ "Home Page for Maestro". Retrieved 25 Feb 2014.
  15. ↑ "Home Page for MAPS".
  16. ↑ "Chime Pro". Symx. Retrieved 24 September 2009.
  17. ↑ "Molden a visualization program of molecular and electronic structure".
  18. ↑ "O 12 Release Notes". Retrieved 24 September 2009.
  19. ↑ Biasini, Marco. "OpenStructure: a flexible software framework for computational structural biology". oxfordjournals.org.
  20. ↑ "Home Page for Procreate". Retrieved 21 March 2011.
  21. ↑ "PyMOL Molecular Viewer". Retrieved 24 September 2009.
  22. ↑ "QMOL". Retrieved 24 September 2009.
  23. ↑ Sayle, RA; Milner-White, EJ (1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. 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". Retrieved 24 September 2009.
  26. ↑ SAMSON Connect
  27. ↑ Scigress commercial license
  28. ↑ "Scigress". fqs.pl. 12 September 2014.
  29. ↑ Spartan webpage
  30. ↑ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  31. ↑ UCSF Chimera license
  32. ↑ 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. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254.
  33. ↑ "UCSF Chimera". Retrieved 24 September 2009.
  34. ↑ 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.
  35. ↑ Visual Molecular Dynamics license
  36. ↑ 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.
  37. ↑ "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009.
  38. ↑ "WHAT IF homepage". Retrieved 24 September 2009.
  39. ↑ "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.
  40. ↑ Reynolds CR, Islam SA, Sternberg MJE (2018). "EzMol: A web server wizard for the rapid visualisation and image production of protein and nucleic acid structures". J Mol Biol. 430 (15): 2244–2248. doi:10.1016/j.jmb.2018.01.013. hdl:10044/1/56880. PMC 5961936. PMID 29391170.
  41. ↑ "RCSB PDB Newsletter".
  42. ↑ Rose, AS; Hildebrand, PW (2015). "NGL Viewer: a web application for molecular visualization". Nucleic Acids Res. 43 (W1): W576–9. doi:10.1093/nar/gkv402. PMC 4489237. PMID 25925569.
  43. ↑ Wade, S (2016). "ProSAT+: visualizing sequence annotations on 3D structure". Protein Eng des Sel. 29 (8): 281–4. doi:10.1093/protein/gzw021. PMID 27284084.
  44. ↑ Hendlich, M (1998). "Databases for protein-ligand complexes". Acta Crystallographica Section D. 54 (Pt 6 Pt 1): 1178–82. doi:10.1107/S0907444998007124. PMID 10089494.
  45. ↑ Wade, S (2017). "TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets". Nucleic Acids Res. 45 (W1): W325–W330. doi:10.1093/nar/gkx277. PMC 5570179. PMID 28431137.
  • Saric, Marc. "Free Molecular Modelling Programs". A rather detailed, objective, and technical assessment of about 20 tools.
  • "PDB list of molecular graphics tools".
  • "Index of Molecular Visualization Resources".
  • "Molecular Visualization Resources by Eric Martz".
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