List of molecular graphics systems
This is a list of notable software systems that are used for visualizing macromolecules.[1]
The tables below indicate which types of data can be visualized in each system:
- EM – Electron microscopy
- HM – Homology modeling
- MD – Molecular dynamics
- MM – Molecular modelling, molecular orbital visualizing
- MRI – Magnetic resonance imaging
- NA – Nucleic acids
- NMR – Nuclear magnetic resonance
- Optical – Optical microscopy
- QM – Quantum chemistry
- SMI – Small molecule interactions
- XRC – X-ray crystallography data such as electron density
| Name | Data | License | Technology | Citations | Comments |
|---|---|---|---|---|---|
| Amira | EM MM MRI Optical SMI XRC | Proprietary[2] | Windows, Linux, Mac | [3] | Based on OpenInventor/OpenGL; focusing on life and biomedical sciences. |
| Ascalaph Designer | MM MD QM | Proprietary | C++ | [4] | Graphics, model building, molecular mechanics, quantum chemistry. |
| Avizo | EM MM MRI Optical SMI XRC | Proprietary[5] | Windows, Linux, Mac | [6] | Avizo is derived from Amira and focusing on materials science. |
| Avogadro | MM XRC MD | Free open-source, GPL | C++, Qt, extensible via Python modules | ||
| Cn3D | Free open-source | Standalone program | [7] | In the NCBI C++ toolkit | |
| Coot | XRC | Free open-source | |||
| Gabedit | XRC MM | Free open-source | C | [8] | |
| Jmol | Free open-source | Java applet or standalone program | [9] | Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry | |
| MDL Chime | Proprietary, free use noncommercial | C++ browser plugin for Windows only | [10] | 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 | [11] | ||
| Molecular Operating Environment (MOE) | HM MD MM NA QM SMI XRC | Proprietary | Windows, Linux, OS X; SVL programming language | Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications. | |
| Molekel | MM XRC | Free open-source | Java 3D applet or standalone program | ||
| PyMOL | XRC SMI EM | open-source, Python | Python | [12] | 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] |
| RasMol | Free open-source | C standalone program | [13][14][15] | ||
| SAMSON | MM MD SMI MRI | Free | Windows, Linux, Mac. C++ (Qt) | [16] | 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[17] | Standalone program | [18] | Edit, visualize and run simulations on various molecular systems. |
| Spartan | MM QM | Proprietary[19] | Standalone program | [20] | 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. |
| UCSF Chimera | XRC SMI EM MD | Proprietary, free use noncommercial[21] | Python | [22][23] | Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[24] |
| VMD | EM MD MM | Proprietary, free use noncommercial[25] | C++ | [26][27] | |
| WHAT IF | HM XRC | Proprietary, shareware for academics | Fortran, C, OpenGL, standalone | [28] | 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 | Proprietary, limited free version | C-assembly, Windows, Linux, Mac | [29] | Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface. |
See also[]
- Biological data visualization
- Comparison of nucleic acid simulation software
- Comparison of software for molecular mechanics modeling
- List of microscopy visualization systems
- List of open-source bioinformatics software
- Molecular graphics
- Molecule editor
References[]
- ^ O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. (March 2010). "Visualization of macromolecular structures". Nature Methods. 7 (3 Suppl): S42-55. doi:10.1038/nmeth.1427. PMC 7097155. PMID 20195256.
- ^ Amira commercial license
- ^ "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.[self-published source?]
- ^ "Ascalaph". Retrieved 24 September 2009.[self-published source?]
- ^ Avizo commercial license
- ^ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.[self-published source?]
- ^ Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (June 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.
- ^ "Gabedit A graphical user interface for computational chemistry packages".
- ^ "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.[self-published source?]
- ^ "Chime Pro". Symx. Retrieved 24 September 2009.[self-published source?]
- ^ "Molden a visualization program of molecular and electronic structure".
- ^ "PyMOL Molecular Viewer". Retrieved 24 September 2009.[self-published source?]
- ^ Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.
- ^ Bernstein HJ (September 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". Retrieved 24 September 2009.[self-published source?]
- ^ SAMSON Connect
- ^ Scigress commercial license
- ^ "Scigress". fqs.pl. 12 September 2014.
- ^ Spartan webpage
- ^ Spartan Tutorial & User's Guide ISBN 1-890661-38-4
- ^ UCSF Chimera license
- ^ Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218.
- ^ "UCSF Chimera". Retrieved 24 September 2009.[self-published source?]
- ^ Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE (July 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.
- ^ Visual Molecular Dynamics license
- ^ Humphrey W, Dalke A, Schulten K (February 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". Retrieved 24 September 2009.[self-published source?]
- ^ "WHAT IF homepage". Retrieved 24 September 2009.[self-published source?]
- ^ "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.[self-published source?]
External links[]
 |
Wikimedia Commons has media related to Molecular visualization softwares. |
- Saric M. "Free Molecular Modelling Programs =". A rather detailed, objective, and technical assessment of about 20 tools.
- "PDB list of molecular graphics tools".
- "Index of Molecular Visualization Resources".
- "Molecular Visualization Resources by Eric Martz".
Categories:
- Bioinformatics software
- Bioinformatics
- Chemistry software
- Lists of software
- Molecular modelling