List of molecular graphics systems Computer Informatics 464 pasar.pts-ptn.net

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.

1 Stand-alone systems
2 Web-based systems
3 See also
4 References
5 External links

Stand-alone systems

Name	Data	License	Technology	Citation	Comments
Ascalaph Graphics	MM MD	free	C++	^[2]
Avizo	EM MM MRI Optical XRC	commercial	Windows, Linux, Mac	^[3]^[4]^[5]
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 MacOS 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.
Cn3D		free	stand-alone application	^[6]^[7]
CheVi	SMI	free	stand-alone application
chemkit	MM MD	free and open-source	C++		Software library for cheminformatics, molecular modelling and visualization.
Coot	XRC MM NA SMI EM	free and open-source	C++, Python, Scheme, GTK+, GSL, OpenGL, Windows, MacOS X, Linux	^[8]	Primarily designed for protein and protein-ligand structure Modeling using X-ray data.
Crystal Studio	MM XRC	commercial	Windows	^[9]	Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
CueMol	MM XRC	free and open-source	Windows, MacOS 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	^[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)
Friend	MM SA MSA	free	Win, 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.
Gabedit	XRC MM	free and open-source	C	^[13]
g0penMol	MD MM	free		^[14]
ICM-Browser		free	Windows,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-source	Java 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, proprietary	C++ browser plugin for Windows only	^[17]	Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol.
Molden	MM XRC			^[18]
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		^[19]
O		free for noncommercial use		^[20]	see also [1]
OpenStructure	EM HM MD MM XRC	free and open-source	Linux, 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		free	C# stand-alone application	^[22]	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	^[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]}
Qmol	MM	free, open-source	C	^[24]	Provided by DNASTAR
RasMol		free and open-source	C stand-alone application	^[25]^[26]^[27]
Sirius		free and open-source	Java3D applet or stand-alone application
SPARTAN	MM QM	commercial	stand-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 Viewer	HM	free and open-source	Java3D applet or stand-alone application	^[29]^[30]	Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
UCSF Chimera	XRC SMI EM MD	free for noncommercial use	Python	^[31]^[32]	Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.^[33]
VMD	EM MD MM	free for noncommercial use	C++	^[34]^[35]
WebMol		free	Java applet and stand-alone	^[36]^[37]	Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IF	HM XRC	shareware for academics	stand-alone	^[38]	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	^[39]	Fully featured molecular modeling and simulation program, incl. structure prediction and docking;

Web-based systems

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	^[40]
WebMol		free	Java applet and stand-alone	^[36]^[37]	Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D Viewer	HM SMI	free and open-source	Java3D applet or stand-alone application	^[29]^[30]	Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
Proteopedia	HM SMI	free	Java applet integrated into web front-end		Integrates 3D structures and different views on those with text descriptions of the structures

References

^ 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.
^ "Ascalaph Graphics". http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Graphics.html. Retrieved 24 September 2009.^{[self-published source?]}
^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". http://www.avizo3d.com. Retrieved August 5, 2010.^{[self-published source?]}
^ "Avizo Official Users' Forum". http://www.mc3dviz.com/avizo-forum/. Retrieved August 5, 2010.^{[self-published source?]}
^ "Avizo - Examples of applications (movies)". http://www.youtube.com/user/Avizo3D. Retrieved August 5, 2010.^{[self-published source?]}
^ 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.
^ "Cn3D Home Page". http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml. Retrieved 28 November 2011.
^ 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.
^ "Crystal Studio". http://www.crystalsoftcorp.com/. Retrieved 24 September 2009.^{[self-published source?]}
^ "Dino Homepage". http://www.dino3d.org/. Retrieved 6 June 2012.
^ 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.
^ "Friend - An Integrated front-end Application for Bioinformatics". http://ilyinlab.org/friend. Retrieved 24 September 2005.^{[self-published source?]}
^ "Gabedit A graphical user interface for computational chemistry packages". http://gabedit.sourceforge.net.
^ "g0penMol". http://www.csc.fi/english/pages/g0penMol. Retrieved 24 September 2009.^{[self-published source?]}
^ http://www.molsoft.com/icm_browser.html
^ "Jmol: an open-source Java viewer for chemical structures in 3D". http://www.jmol.org. Retrieved 24 September 2009.^{[self-published source?]}
^ "Chime Pro". Symx. http://www.symyx.com/products/software/cheminformatics/chime-pro/index.jsp. Retrieved 24 September 2009.^{[self-published source?]}
^ "MOLDEN a visualization program of molecular and electronic structure". http://www.cmbi.ru.nl/molden/molden.html.
^ "NOC Homepage". http://noch.sourceforge.net/. Retrieved 24 September 2009.^{[self-published source?]}
^ "O 12 Release Notes". http://xray.bmc.uu.se/alwyn/Distribution/ov11_12/ov12.html. Retrieved 24 September 2009.^{[self-published source?]}
^ 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
^ "Home Page for Procreate". http://members.iinet.net.au/~lahg/procreate/. Retrieved 21 March 2011.^{[self-published source?]}
^ "PyMOL Molecular Viewer - Home Page". http://www.pymol.org. Retrieved 24 September 2009.^{[self-published source?]}
^ "QMOL". http://www.dnastar.com/qmol/. Retrieved 24 September 2009.^{[self-published source?]}
^ 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.
^ 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.
^ "Home Page for RasMol and OpenRasMol". http://www.rasmol.org/. Retrieved 24 September 2009.^{[self-published source?]}
^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
^ ^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.
^ ^a ^b "General information about SRS 3D". http://srs3d.org/About/. Retrieved 24 September 2009.^{[self-published source?]}
^ 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.
^ "UCSF Chimera". http://www.cgl.ucsf.edu/chimera. Retrieved 24 September 2009.^{[self-published source?]}
^ 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/PMC1570152/.
^ 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.
^ "VMD - Visual Molecular Dynamics". http://www.ks.uiuc.edu/Research/vmd. Retrieved 24 September 2009.^{[self-published source?]}
^ ^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.
^ ^a ^b "WebMol Java PDB Viewer". http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl. Retrieved 24 September 2009.^{[unreliable source?]}
^ "WHAT IF homepage". http://swift.cmbi.ru.nl/whatif. Retrieved 24 September 2009.^{[self-published source?]}
^ "YASARA - Yet Another Scientific Artificial Reality Application". http://www.yasara.org. Retrieved 24 September 2009.^{[self-published source?]}
^ 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

Saric, Marc. "Free Molecular Modelling Programs". http://www.marcsaric.de/index.php/Free_Molecular_Modelling_Programs. A rather detailed, objective, and technical assessment of about 20 tools.
"PDB list of molecular graphics tools". http://www.rcsb.org/pdb/static.do?p=software/software_links/molecular_graphics.html.
"World Index of Molecular Visualization Resources". http://www.molvisindex.org.
"Molecular Visualization Resources by Eric Martz". http://molviz.org.

List of molecular graphics systems

Contents

Stand-alone systems

Web-based systems

See also

References

External links