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Daftar/Tabel -- molecular graphics systems

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.

Contents

Stand-alone systems

NameDataLicenseTechnologyCitationComments
Ascalaph GraphicsMM MDfreeC++[2] 
AvizoEM MM MRI Optical XRCcommercialWindows, Linux, Mac[3][4][5] 
AvogadroMM XRC MDfree and open-sourceC++/Qt, can be extended with Python modules  
BALLViewMM Nucleic Acids XRC SMIfree and open-source, GPLC++ and Python; Windows, Linux, Solaris, and MacOS XBALL projectBALLView uses OpenGL and the real time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes.
Cn3D freestand-alone application[6][7] 
CheViSMIfreestand-alone application  
chemkitMM MDfree and open-sourceC++ Software library for cheminformatics, molecular modelling and visualization.
CootXRC MM NA SMI EMfree and open-sourceC++, Python, Scheme, GTK+, GSL, OpenGL, Windows, MacOS X, Linux[8]Primarily designed for protein and protein-ligand structure Modeling using X-ray data.
Crystal StudioMM XRCcommercialWindows[9]Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
CueMolMM XRCfree and open-sourceWindows, MacOS X, and Linux application based on OpenGL and Mozilla XULRunner.  
DenebMD MMCommercial, Trial version availableLinux and Windows Graphical User Interface and builders for relevant Calculation packages (SIESTA, VASP, QE, etc)...
DinoEM MD MM XRCfreeLinux and OSX[10]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)
FriendMM SA MSAfreeWin, Linux[11][12]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.
GabeditXRC MMfree and open-sourceC[13] 
g0penMolMD MMfree [14] 
ICM-Browser freeWindows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery[15]multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots
Jmol free and open-sourceJava applet or stand-alone application[16]Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime free for noncommercial use, proprietaryC++ browser plugin for Windows only[17]Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol. 
MoldenMM XRC  [18] 
MOEMM XRCcommercial Molecular Operating Environment (MOE) 
MolekelMM XRCfree and open-sourceJava3D applet or stand-alone application[citation needed] 
NOCH free and open-source [19] 
O free for noncommercial use [20]see also [1]
OpenStructureEM HM MD MM XRCfree and open-sourceLinux, OSX and Windows[21]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 freeC# stand-alone application[22]Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects
PyMOLXRC SMI EMfree for noncommercial use, open-sourcePython[23]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]
QmolMMfree, open-sourceC[24]Provided by DNASTAR
RasMol free and open-sourceC stand-alone application[25][26][27] 
Sirius free and open-sourceJava3D applet or stand-alone application  
SPARTANMM QMcommercialstand-alone application[28]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 ViewerHMfree and open-sourceJava3D applet or stand-alone application[29][30]Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
UCSF ChimeraXRC SMI EM MDfree for noncommercial usePython[31][32]Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[33]
VMDEM MD MMfree for noncommercial useC++[34][35] 
WebMol freeJava applet and stand-alone[36][37]Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IFHM XRCshareware for academicsstand-alone[38]Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
YASARAHM NMR XRCcommercial; free version for elementary structure workC/Assembler, graphical or text mode (clusters), Python interface, Windows, Linux, Mac[39]Fully featured molecular modeling and simulation program, incl. structure prediction and docking;

Web-based systems

NameDataLicenseTechnologyCitationComments
GLmolMM XRCfree and open-sourceJavascript, WebGL, HTML5 Doesn't need Java or plugins. Runs on Firefox, Google Chrome, Safari and some Android devices.
RelibaseSMIpartly free (full functionality requires a license)Java applet integrated into web front-end[40] 
WebMol freeJava applet and stand-alone[36][37]Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D ViewerHMSMIfree and open-sourceJava3D applet or stand-alone application[29][30]Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
ProteopediaHMSMIfreeJava applet integrated into web front-end Integrates 3D structures and different views on those with text descriptions of the structures

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 Graphics". http://www.biomolecular-modeling.com/ Ascalaph/Ascalaph_Graphics.html. Retrieved 24 September 2009.[self-published source?]
  3. ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". http://www.avizo3d.com. Retrieved August 5, 2010.[self-published source?]
  4. ^ "Avizo Official Users' Forum". http://www.mc3dviz.com/avizo-forum/. Retrieved August 5, 2010.[self-published source?]
  5. ^ "Avizo - Examples of applications (movies)". http://www.youtube.com/user/Avizo3D. Retrieved August 5, 2010.[self-published source?]
  6. ^ 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.
  7. ^ "Cn3D Home Page". http://www.ncbi.nlm.nih.gov/Structure /CN3D/cn3d.shtml. Retrieved 28 November 2011.
  8. ^ 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.
  9. ^ "Crystal Studio". http://www.crystalsoftcorp.com/. Retrieved 24 September 2009.[self-published source?]
  10. ^ "Dino Homepage". http://www.dino3d.org/. Retrieved 6 June 2012.
  11. ^ 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.
  12. ^ "Friend - An Integrated front-end Application for Bioinformatics". http://ilyinlab.org/friend. Retrieved 24 September 2005.[self-published source?]
  13. ^ "Gabedit A graphical user interface for computational chemistry packages". http://gabedit.sourceforge.net.
  14. ^ "g0penMol". http://www.csc.fi/english/pages/g0pen Mol. Retrieved 24 September 2009.[self-published source?]
  15. ^ http://www.molsoft.com/icm_browser.ht ml
  16. ^ "Jmol: an open-source Java viewer for chemical structures in 3D". http://www.jmol.org. Retrieved 24 September 2009.[self-published source?]
  17. ^ "Chime Pro". Symx. http://www.symyx.com/products/softwar e/cheminformatics/chime-pro/index.jsp. Retrieved 24 September 2009.[self-published source?]
  18. ^ "MOLDEN a visualization program of molecular and electronic structure". http://www.cmbi.ru.nl/molden/molden.h tml.
  19. ^ "NOC Homepage". http://noch.sourceforge.net/. Retrieved 24 September 2009.[self-published source?]
  20. ^ "O 12 Release Notes". http://xray.bmc.uu.se/alwyn/Distribut ion/ov11_12/ov12.html. Retrieved 24 September 2009.[self-published source?]
  21. ^ 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
  22. ^ "Home Page for Procreate". http://members.iinet.net.au/~lahg/pro create/. Retrieved 21 March 2011.[self-published source?]
  23. ^ "PyMOL Molecular Viewer - Home Page". http://www.pymol.org. Retrieved 24 September 2009.[self-published source?]
  24. ^ "QMOL". http://www.dnastar.com/qmol/. Retrieved 24 September 2009.[self-published source?]
  25. ^ 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.
  26. ^ 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.
  27. ^ "Home Page for RasMol and OpenRasMol". http://www.rasmol.org/. Retrieved 24 September 2009.[self-published source?]
  28. ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  29. ^ 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.
  30. ^ a b "General information about SRS 3D". http://srs3d.org/About/. Retrieved 24 September 2009.[self-published source?]
  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". http://www.cgl.ucsf.edu/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 1570152. PMID 16836757. //www.ncbi.nlm.nih.gov/pmc/articles/P MC1570152/.
  34. ^ 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.
  35. ^ "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd. Retrieved 24 September 2009.[self-published source?]
  36. ^ 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.
  37. ^ a b "WebMol Java PDB Viewer". http://www.cmpharm.ucsf.edu/cgi-bin/w ebmol.pl. Retrieved 24 September 2009.[unreliable source?]
  38. ^ "WHAT IF homepage". http://swift.cmbi.ru.nl/whatif. Retrieved 24 September 2009.[self-published source?]
  39. ^ "YASARA - Yet Another Scientific Artificial Reality Application". http://www.yasara.org. Retrieved 24 September 2009.[self-published source?]
  40. ^ 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

(Sebelumnya) List of model checking toolsList of MorphOS bundled applic ... (Berikutnya)