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 XRC MM Proprietary, free use noncommercial Java, Java 3D, Solaris, SPARC, Windows, Linux [3] A molecular visualization software package based on Zeus, mainly designed to use the Java-3d visualisation core to output high quality graphics. Supports file formats: PDB, MOL, XYZ.[4] operating system, and Windows and Linux via Java (JVM).
Avizo EM MM MRI Optical XRC Proprietary[5] Windows, Linux, Mac [6][7][8]
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 BALL project 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.
Cn3D Free open-source Standalone program [9][10]
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+, GSL, OpenGL, Windows, Mac OS X, Linux [11] Designed mostly for protein and protein-ligand structure modeling via X-ray data.
Crystal Studio MM XRC Proprietary[12] Windows [13] 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, Mac OS X, Linux, application based on OpenGL and Mozilla 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 [14] Aims to visualize many types structural data in one program and allow users to explore relationships between data. 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). Output can be written as PNG, PostScript, and POV-Ray (v3.1 and v3.5)
DRAWxtl Free open-source Linux, openVMS, OS X, Windows
Friend MM SA MSA Free open-source Win, Linux [15][16] 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.
GDIS Free open-source display, manipulation, and analysis of isolated molecules and periodic structures.
Gabedit XRC MM Free open-source C [17]
g0penMol MD MM Free open-source [18]
GPView QM MD Free open-source 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, fast C++ graphics, free plugin and activeICM for Web delivery [19] multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots
Jmol Free open-source Java applet or standalone program [20] 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[21] C++, Qt, Python API [22]
MDL Chime Proprietary, free use noncommercial, proprietary C++ browser plugin for Windows only [23] Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol.
Molden MM XRC Proprietary, free use academic [24]
Molgif Free open-source Go An easy-to-use tool to create GIF animations of molecules
Molecular Operating Environment (MOE) MM XRC Proprietary Molecular Operating Environment (MOE)
Molekel MM XRC Free open-source Java 3D applet or standalone program [citation needed]
MView MM XRC MD Free open-source C++, Python, GTK+; Linux
O Proprietary, free use noncommercial [25] see also [2]
OpenStructure EM HM MD MM XRC Free open-source Linux, OS X, Windows [26] 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 Free open-source C# standalone program [27] 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 [28] 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 MM Free open-source C [29] Provided by DNASTAR
RasMol Free open-source C standalone program [30][31][32]
SAMSON MM MD SMI Free[33] Windows, Linux, Mac. C++ (Qt) SAMSON Connect 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[34] Standalone program [35] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary[36] Standalone program [37] 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 open-source Java 3D applet or standalone program [38][39] Integrates 3D structures with sequence and feature data: domains, SNPs, etc.
UCSF Chimera XRC SMI EM MD Proprietary, free use noncommercial[40] Python [41][42] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[43]
VMD EM MD MM Proprietary, free use noncommercial[44] C++ [45][46]
Vimol MM MD Free open-source C Powerful molecular building and trajectory visualization package with vi-like interface.
VESTA Free open-source Crystal structure visualization and computation
V_Sim Free open-source GTK+; Linux, OS X, Windows
WebMol Free open-source Java applet and standalone [47][48] Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IF HM XRC Proprietary, shareware for academics standalone [49] 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 [50] crystalline and molecular structure visualisation program;
YASARA HM NMR XRC Proprietary, free version for elementary structure work C-assembly, graphical or text mode (clusters), Python interface, Windows, Linux, Mac [51] Fully featured molecular modeling and simulation program, incl., structure prediction and docking
Zeus XRC MM Proprietary, free use noncommercial Delphi, OpenGL [52] A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics. Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral angles can be generated and exported. PDB files can be automatically downloaded from the RSCB PDB. A Java version (Zeus-Java) is also available for Linux/Windows"Molecular Graphics Software at RCSB.org". Retrieved 2 January 2014. 

Web-based systems[edit]

Name Data License Technology Citations Comments
GLmol MM XRC Free open-source JavaScript, WebGL, HTML5 Doesn't need Java or plugins. Runs on Firefox, Google Chrome, Safari and some Android devices.
iCn3D MM XRC Free open-source JavaScript, WebGL, HTML5 No install needed, runs on most web browsers and mobile devices. Has many features. Any custom display can be reproduced with a URL via Share Link option.
Relibase SMI Proprietary, part free, full function needs license Java applet integrated into web front-end [53]
Prosat+ XRC,NMR Free open-source JavaScript, WebGL, HTML5, JSMol [54] Display of UniProt features on protein structures possible. Annotations on the structure can be send or published via URL. Similar structures can be searched and their annotations displayed.
WebMol Free open-source Java applet and standalone [47][48] Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D Viewer HMSMI Free open-source Java 3D applet or standalone program [38][39] Integrates 3D structures with sequence and feature data: domains, SNPs, etc.
Proteopedia HMSMI Free open-source Java applet integrated into web front-end Integrates 3D structures and different views on those with text descriptions of structures

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. ^ "Athena molecular viewer". Retrieved 4 March 2014. [self-published source?]
  4. ^ "Athena supports the SPARC processor and Solaris 10". Retrieved 4 March 2014. 
  5. ^ Avizo commercial license
  6. ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". Retrieved August 5, 2010. [self-published source?]
  7. ^ "Avizo Official Users' Forum". Retrieved August 5, 2010. [self-published source?]
  8. ^ "Avizo - Examples of applications (movies)". Retrieved August 5, 2010. [self-published source?]
  9. ^ 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. 
  10. ^ "Cn3D Home Page". Retrieved 28 November 2011. 
  11. ^ 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. 
  12. ^ Crystal Studio commercial license
  13. ^ "Crystal Studio". Retrieved 24 September 2009. [self-published source?]
  14. ^ "Dino". Retrieved 6 June 2012. 
  15. ^ 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. 
  16. ^ "Friend - An Integrated front-end Application for Bioinformatics". Retrieved 24 September 2005. [self-published source?]
  17. ^ "Gabedit A graphical user interface for computational chemistry packages". 
  18. ^ "g0penMol". Retrieved 24 September 2009. [self-published source?]
  19. ^ "Molsoft L.L.C.: ICM-Browser". molsoft.com. 
  20. ^ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009. [self-published source?]
  21. ^ Schrödinger Maestro, free use academic
  22. ^ "Home Page for Maestro". Retrieved 25 Feb 2014. [self-published source?]
  23. ^ "Chime Pro". Symx. Retrieved 24 September 2009. [self-published source?]
  24. ^ "Molden a visualization program of molecular and electronic structure". 
  25. ^ "O 12 Release Notes". Retrieved 24 September 2009. [self-published source?]
  26. ^ Biasini, Marco. "OpenStructure: a flexible software framework for computational structural biology". oxfordjournals.org. 
  27. ^ "Home Page for Procreate". Retrieved 21 March 2011. [self-published source?]
  28. ^ "PyMOL Molecular Viewer". Retrieved 24 September 2009. [self-published source?]
  29. ^ "QMOL". Retrieved 24 September 2009. [self-published source?]
  30. ^ 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. 
  31. ^ 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. 
  32. ^ "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009. [self-published source?]
  33. ^ SAMSON Connect
  34. ^ Scigress commercial license
  35. ^ "Scigress". fqs.pl. 12 September 2014. 
  36. ^ Spartan webpage
  37. ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  38. ^ 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. 
  39. ^ a b "General information about SRS 3D". Retrieved 24 September 2009. [self-published source?]
  40. ^ UCSF Chimera license
  41. ^ 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. 
  42. ^ "UCSF Chimera". Retrieved 24 September 2009. [self-published source?]
  43. ^ 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. 
  44. ^ Visual Molecular Dynamics license
  45. ^ 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. 
  46. ^ "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009. [self-published source?]
  47. ^ 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. 
  48. ^ a b "WebMol Java PDB Viewer". Retrieved 24 September 2009. [unreliable source?]
  49. ^ "WHAT IF homepage". Retrieved 24 September 2009. [self-published source?]
  50. ^ "XCrySDen". Retrieved 17 February 2015. 
  51. ^ "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009. [self-published source?]
  52. ^ "Zeus Molecular Viewer". Retrieved 5 November 2011. [self-published source?]"Molecular Graphics Software at RCSB.org". Retrieved 2 January 2014. 
  53. ^ 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. 
  54. ^ Wade, S (2016). "ProSAT+: visualizing sequence annotations on 3D structure.". Protein Eng Des Sel. doi:10.1093/protein/gzw021. PMID 27284084. 

External links[edit]