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 indicates which types of data can be visualized in each system: EM = Electron microscopy; HM = Homology modelling; MD = Molecular Dynamics; MM = Molecular modelling and molecular orbital visualization; MRI = Magnetic resonance imaging; NA = Nucleic Acids; NMR = nuclear magnetic resonance; Optical = Optical microscopy; SMI = Small molecule interactions; XRC = X-ray crystallography data such as electron density.

Stand-alone systems[edit]

Name Data License Technology Citation Comments
Ascalaph Designer MM MD free C++ [2] Graphics, model building, molecular mechanics and quantum chemistry.
Athena XRC MM free for noncommercial use Java/Java3d/Solaris/SPARC/Windows/Linux [3] A molecular visualization software package based on Zeus, primarily designed to utilise the Java-3d visualisation core to output high quality molecular graphics. Athena supports PDB, MOL, and XYZ file formats. "Athena supports the SPARC processor and Solaris 10". Retrieved 4 March 2014.  operating system as well as MS Windows and Linux through the use of Java (JVM).
Avizo EM MM MRI Optical XRC commercial Windows, Linux, Mac [4][5][6]
Avogadro MM XRC MD free and open-source C++/Qt, can be extended with Python modules
BALLView MM Nucleic Acids XRC SMI free and open-source, GPL C++ and Python; Windows, Linux, Solaris, and Mac OS X BALL project BALLView uses OpenGL and the real-time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes.
CAVER Analyst MD EM XRC free for noncommercial use Java ; Windows, Linux, Solaris, and Mac OS X [1] CAVER Analyst is the protein tunnel analysis software that delivers immediate results that matters for protein engineers and structural biologists. It combines the CAVER algorithm with advanced visualization methods in the easy to use software to obtain the results faster.
Cn3D free stand-alone application [7][8]
CheVi SMI free stand-alone application
chemkit MM MD free and open-source C++ Software library for cheminformatics, molecular modelling and visualization.
chemlab MM MD free and open-source Python Extensible molecular 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 and open-source C++, Python, Scheme, GTK+, GSL, OpenGL, Windows, Mac OS X, Linux [9] Primarily designed for protein and protein-ligand structure Modeling using X-ray data.
Crystal Studio MM XRC commercial Windows [10] Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
CueMol MM XRC free and open-source Windows, Mac OS X, and Linux application based on OpenGL and Mozilla XULRunner.
Deneb MD MM Commercial, Trial version available Linux and Windows Graphical User Interface and builders for relevant Calculation packages (SIESTA, VASP, QE, etc.)...
Dino EM MD MM XRC free Linux and OSX [11] Aims to visualize many types structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). Output can be written as PNG, PostScript and POV-Ray (v3.1 and v3.5)
Friend MM SA MSA free Win, Linux [12][13] 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.
Gabedit XRC MM free and open-source C [14]
g0penMol MD MM free [15]
ICM-Browser free Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery [16] multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots
Jmol free and open-source Java applet or stand-alone application [17] 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 commercial, free for academics C++/Qt, Python API [18]
MDL Chime free for noncommercial use, proprietary C++ browser plugin for Windows only [19] Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol.
Molden MM XRC [20]
MOE MM XRC commercial Molecular Operating Environment (MOE)
Molekel MM XRC free and open-source Java3D applet or stand-alone application [citation needed]
NOCH free and open-source [21]
MView MM XRC MD free C++, Python, and GTK+; Linux
O free for noncommercial use [22] see also [2]
OpenStructure EM HM MD MM XRC free and open-source Linux, OSX and Windows [23] Computational Structural Biology Framework in C++ and Python, aimed at users and developers, high-end visualization of atomic structures, electron densities and molecular trajectories.
Procreate free C# stand-alone application [24] Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects
PyMOL XRC SMI EM free for noncommercial use, open-source Python [25] According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.[citation needed]
Qmol MM free, open-source C [26] Provided by DNASTAR
RasMol free and open-source C stand-alone application [27][28][29]
Sirius free and open-source Java3D applet or stand-alone application
SCIGRESS MM QM commercial stand-alone application [30] Edit, visualize and run simulations on various molecular systems.
SPARTAN MM QM commercial stand-alone application [31] 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 and open-source Java3D applet or stand-alone application [32][33] Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
UCSF Chimera XRC SMI EM MD free for noncommercial use Python [34][35] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[36]
VMD EM MD MM free for noncommercial use C++ [37][38]
Vimol MM MD free and open-source C Powerful molecular building and trajectory visualization package with vi-like interface.
WebMol free Java applet and stand-alone [39][40] Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IF HM XRC shareware for academics stand-alone [41] 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 commercial; free version for elementary structure work C/Assembler, graphical or text mode (clusters), Python interface, Windows, Linux, Mac [42] Fully featured molecular modeling and simulation program, incl. structure prediction and docking;
Zeus XRC MM free for noncommercial use Delphi/OpenGL [43] 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 Citation Comments
GLmol MM XRC free and open-source JavaScript, WebGL, HTML5 Doesn't need Java or plugins. Runs on Firefox, Google Chrome, Safari and some Android devices.
Relibase SMI partly free (full functionality requires a license) Java applet integrated into web front-end [44]
WebMol free Java applet and stand-alone [39][40] Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D Viewer HMSMI free and open-source Java3D applet or stand-alone application [32][33] Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
Proteopedia HMSMI free Java applet integrated into web front-end Integrates 3D structures and different views on those with text descriptions of the 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. ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". Retrieved August 5, 2010. [self-published source?]
  5. ^ "Avizo Official Users' Forum". Retrieved August 5, 2010. [self-published source?]
  6. ^ "Avizo - Examples of applications (movies)". Retrieved August 5, 2010. [self-published source?]
  7. ^ 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. 
  8. ^ "Cn3D Home Page". Retrieved 28 November 2011. 
  9. ^ 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. 
  10. ^ "Crystal Studio". Retrieved 24 September 2009. [self-published source?]
  11. ^ "Dino Homepage". Retrieved 6 June 2012. 
  12. ^ 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. 
  13. ^ "Friend - An Integrated front-end Application for Bioinformatics". Retrieved 24 September 2005. [self-published source?]
  14. ^ "Gabedit A graphical user interface for computational chemistry packages". 
  15. ^ "g0penMol". Retrieved 24 September 2009. [self-published source?]
  16. ^ http://www.molsoft.com/icm_browser.html
  17. ^ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009. [self-published source?]
  18. ^ "Home Page for Maestro". Retrieved 25 Feb 2014. [self-published source?]
  19. ^ "Chime Pro". Symx. Retrieved 24 September 2009. [self-published source?]
  20. ^ "MOLDEN a visualization program of molecular and electronic structure". 
  21. ^ "NOC Homepage". Retrieved 24 September 2009. [self-published source?]
  22. ^ "O 12 Release Notes". Retrieved 24 September 2009. [self-published source?]
  23. ^ M. Biasini, V. Mariani, J. Haas, S. Scheuber, A.D. Schenk, T. Schwede and A. Philippsen OpenStructure: A flexible software framework for computational structural biology, Bioinformatics, 2010
  24. ^ "Home Page for Procreate". Retrieved 21 March 2011. [self-published source?]
  25. ^ "PyMOL Molecular Viewer - Home Page". Retrieved 24 September 2009. [self-published source?]
  26. ^ "QMOL". Retrieved 24 September 2009. [self-published source?]
  27. ^ Sayle, RA; Milner-White, EJ (1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences 20 (9): 374. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707. 
  28. ^ 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. 
  29. ^ "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009. [self-published source?]
  30. ^ About SCIGRESS
  31. ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  32. ^ 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. 
  33. ^ a b "General information about SRS 3D". Retrieved 24 September 2009. [self-published source?]
  34. ^ 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. 
  35. ^ "UCSF Chimera". Retrieved 24 September 2009. [self-published source?]
  36. ^ 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. 
  37. ^ 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. 
  38. ^ "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009. [self-published source?]
  39. ^ 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. 
  40. ^ a b "WebMol Java PDB Viewer". Retrieved 24 September 2009. [unreliable source?]
  41. ^ "WHAT IF homepage". Retrieved 24 September 2009. [self-published source?]
  42. ^ "YASARA - Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009. [self-published source?]
  43. ^ "Zeus Molecular Viewer - Home Page". Retrieved 5 November 2011. [self-published source?]"Molecular Graphics Software at RCSB.org". Retrieved 2 January 2014. 
  44. ^ Hendlich, M (1998). "Databases for protein-ligand complexes". Acta crystallographica. Section D, Biological crystallography 54 (Pt 6 Pt 1): 1178–82. doi:10.1107/S0907444998007124. PMID 10089494. 

External links[edit]