List of molecular graphics systems

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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[edit]

Name Data License Technology Citations Comments
Ascalaph Designer MM MD QM Free open-source 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 [1] 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.
Cn3D Free open-source Standalone program [5]
CheVi[dead link] 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[dead link] 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).
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 Display, manipulate, and analyze isolated molecules and periodic structures.
Gabedit XRC MM Free open-source C [9]
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.
ICM-Browser Free open source Windows, Mac, Linux, C++ [10] Multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots. Plugin and activeICM for Web delivery.
Jmol Free open-source Java applet or standalone program [11] 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[12] C++, Qt, Python API [13]
MAPS MM QM MD SMI XRC Optical Proprietary C++, Python API [14] 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 [15] 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 [16]
Molgif Free open-source Go An easy-to-use tool to create GIF animations of molecules
Molecular Operating Environment (MOE) MM XRC Proprietary
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 [17] see also [2]
OpenStructure EM HM MD MM XRC Free open-source Linux, OS X, Windows [18] 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[dead link] Free open-source Fortran Ball-and-stick type illustrations
Procreate Proprietary C# standalone program [19] 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 [20] 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]
Qmol[dead link] MM Free open-source C [21] Provided by DNASTAR
RasMol Free open-source C standalone program [22][23][24]
SAMSON MM MD SMI Free Windows, Linux, Mac. C++ (Qt) [25] 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[26] Standalone program [27] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary[28] Standalone program [29] 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[30] Python [31][32] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[33]
VMD EM MD MM Proprietary, free use noncommercial[34] C++ [35][36]
Vimol MM MD Free open-source C Powerful molecular building and trajectory visualization package with vi-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 [37] 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 [38] Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Web-based systems[edit]

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.
GLmol MM XRC Free open-source JavaScript, WebGL, HTML5 Early WebGL viewer,[39] not actively developed anymore.
iCn3D MM XRC Free open-source JavaScript, WebGL, HTML5 Any custom display can be reproduced with a URL via Share Link option.
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 Many representations of biomolecules. Used by RCSB PDB.
Prosat+ XRC, NMR Free JavaScript, WebGL, HTML5, JSMol [40] 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 [41] Login required to see the website.
Speck Free open-source JavaScript, WebGL Reads only xyz files. Specialized in ambient occlusion.
UglyMol XRC Free open-source JavaScript, WebGL Specialized in presenting protein models with electron density maps.

See also[edit]

References[edit]

  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. [self-published source?]
  3. ^ Avizo commercial license
  4. ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". Retrieved August 5, 2010. [self-published source?]
  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. 18 (21): 3677–8. doi:10.1093/bioinformatics/bti602. PMID 16076889. 
  9. ^ "Gabedit A graphical user interface for computational chemistry packages". 
  10. ^ "Molsoft L.L.C.: ICM-Browser". molsoft.com. 
  11. ^ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009. [self-published source?]
  12. ^ Schrödinger Maestro, free use academic
  13. ^ "Home Page for Maestro". Retrieved 25 Feb 2014. [self-published source?]
  14. ^ "Home Page for MAPS". 
  15. ^ "Chime Pro". Symx. Retrieved 24 September 2009. [self-published source?]
  16. ^ "Molden a visualization program of molecular and electronic structure". 
  17. ^ "O 12 Release Notes". Retrieved 24 September 2009. [self-published source?]
  18. ^ Biasini, Marco. "OpenStructure: a flexible software framework for computational structural biology". oxfordjournals.org. 
  19. ^ "Home Page for Procreate". Retrieved 21 March 2011. [self-published source?]
  20. ^ "PyMOL Molecular Viewer". Retrieved 24 September 2009. [self-published source?]
  21. ^ "QMOL". Retrieved 24 September 2009. [self-published source?]
  22. ^ 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. 
  23. ^ 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. 
  24. ^ "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009. [self-published source?]
  25. ^ SAMSON Connect
  26. ^ Scigress commercial license
  27. ^ "Scigress". fqs.pl. 12 September 2014. 
  28. ^ Spartan webpage
  29. ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  30. ^ UCSF Chimera license
  31. ^ 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. 
  32. ^ "UCSF Chimera". Retrieved 24 September 2009. [self-published source?]
  33. ^ 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 1570152Freely accessible. PMID 16836757. 
  34. ^ Visual Molecular Dynamics license
  35. ^ 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. 
  36. ^ "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009. [self-published source?]
  37. ^ "WHAT IF homepage". Retrieved 24 September 2009. [self-published source?]
  38. ^ "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009. [self-published source?]
  39. ^ http://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2012q4/education-corner.html
  40. ^ Wade, S (2016). "ProSAT+: visualizing sequence annotations on 3D structure.". Protein Eng Des Sel. doi:10.1093/protein/gzw021. PMID 27284084. 
  41. ^ 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. 

External links[edit]