List of molecular graphics systems

Last updated

This is a list of notable software systems that are used for visualizing macromolecules. [1]

Contents

NameDataLicenseTechnologyCitationsComments
Amira EM MM MRI Optical SMI XRD Proprietary [2] Windows, Linux, Mac [3] [ self-published source? ]Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ [4] [ self-published source? ]Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRD Proprietary [5] Windows, Linux, Mac [6] [ self-published source? ]Avizo is derived from Amira and focusing on materials science.
Avogadro MM XRD MD Free open-source, GPL C++, Qt, extensible via Python modules
BALL Molecular dynamics MM NMR LGPL open-source Standalone program [7]
Cn3D Free open-source Standalone program [8] In the NCBI C++ toolkit
Coot XRD Free open-source
Gabedit XRD MM Free open-source C [9]
Jmol Free open-source Java (applet or standalone program)
Transpiled HTML5/JavaScript for browser		 [10] [ self-published source? ]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 [11] [ self-published source? ]Build and visualize molecule and periodic systems (crystal, structures, fluids...), animate trajectories, visualize molecular orbitals, density, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors.
Mol* MM MD NA SMI XRD Free open-source (MIT) TypeScript (WebGL, React) [12] Viewer currently used by RCSB-PDB and EMBL/PDBe. Contains a scripting language.
Molden MM XRD Proprietary, free use academic [13]
Molecular Operating Environment (MOE) HM MD MM NA QM SMI XRD Proprietary Windows, Linux, OS X; SVL programming languageBuild, 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 XRD Free open-source Java 3D applet or standalone program
PyMOL MM XRD SMI EM Open-source [14] Python [15] [ self-published source? ]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 [16] [17] [18] [ self-published source? ]
SAMSON MM MD SMI MRI Proprietary, limited free versionWindows, Linux, Mac. C++ (Qt) [19] Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Sirius Free open-source Java 3D applet or standalone program No longer supported as of 2011.
Scigress MM QM Proprietary [20] Standalone program [21] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary [22] Standalone program [23] 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 XRD SMI EM MD Free open-source [24] for noncommercial use [25] Python [26] [27] [ self-published source? ]Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses. [28]
VMD EM MD MM Free open-source for noncommercial use [29] C++ [30] [31] [ self-published source? ]
WHAT IF HM XRD Proprietary, shareware for academics Fortran, C, OpenGL, standalone [32] [ self-published source? ]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 [33] [ self-published source? ]Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Key

The tables below indicate which types of data can be visualized in each system:

See also

Related Research Articles

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

<span class="mw-page-title-main">Post-translational modification</span> Biological processes

Post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes translating mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.

<span class="mw-page-title-main">Structural bioinformatics</span> Bioinformatics subfield

Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.

<span class="mw-page-title-main">Kinemage</span>

A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can also represent other types of 3-dimensional data. The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the file extension '.kin'.

<span class="mw-page-title-main">Visual Molecular Dynamics</span> Visualization and modelling software

Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.

<span class="mw-page-title-main">RasMol</span> Software for the visualisation of macromolecules

RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 1990s.

<span class="mw-page-title-main">PyMOL</span> Proprietary open-sourced python biology structure tool for visualisation

PyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license, and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format.

<span class="mw-page-title-main">UCSF Chimera</span>

UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.

<span class="mw-page-title-main">BALL</span>

BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.

The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.

Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins, termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved.

<span class="mw-page-title-main">Ribbon diagram</span> 3D schematic representation of protein structure

Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organisation of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure, such as the balls for the oxygen atoms attached to myoglobin's active site in the adjacent figure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.

<span class="mw-page-title-main">Molecular models of DNA</span>

Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.

<span class="mw-page-title-main">Avogadro (software)</span>

Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.

Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).

<span class="mw-page-title-main">Amira (software)</span> Software platform for 3D and 4D data visualization

Amira is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.

<span class="mw-page-title-main">SAMSON</span>

SAMSON is a computer software platform for molecular design being developed by OneAngstrom and previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA).

References

  1. ↑ 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.
  2. ↑ Amira commercial license
  3. ↑ "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.
  4. ↑ "Ascalaph" . Retrieved 24 September 2009.
  5. ↑ Avizo commercial license
  6. ↑ "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.
  7. ↑ Hildebrandt, Andreas (25 October 2010). "BALL - biochemical algorithms library 1.3". BMC Bioinformatics. 11: 531. Retrieved 14 June 2022.
  8. ↑ 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.
  9. ↑ "Gabedit A graphical user interface for computational chemistry packages".
  10. ↑ "Jmol: an open-source Java viewer for chemical structures in 3D" . Retrieved 24 September 2009.
  11. ↑ "Chime Pro". Symx. Retrieved 24 September 2009.
  12. ↑ Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodová, Radka; Berka, Karel; Bazgier, Václav; Velankar, Sameer; Burley, Stephen K; Koča, Jaroslav; Rose, Alexander S (2 July 2021). "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures". Nucleic Acids Research. 49 (W1): W431–W437. doi:10.1093/nar/gkab314. PMC   8262734 .
  13. ↑ "Molden a visualization program of molecular and electronic structure".
  14. ↑ "PyMOL License". Jan 8, 2010. Retrieved 2023-03-27.
  15. ↑ "PyMOL Molecular Viewer" . Retrieved 24 September 2009.
  16. ↑ 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.
  17. ↑ 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.
  18. ↑ "Home Page for RasMol and OpenRasMol" . Retrieved 24 September 2009.
  19. ↑ SAMSON Connect
  20. ↑ Scigress commercial license
  21. ↑ "Scigress". fqs.pl. 12 September 2014.
  22. ↑ Spartan webpage
  23. ↑ Spartan Tutorial & User's Guide ISBN   1-890661-38-4
  24. ↑ "UCSF Chimera code repository". www.rbvi.ucsf.edu. Retrieved 2023-03-27.
  25. ↑ UCSF Chimera license
  26. ↑ 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.
  27. ↑ "UCSF Chimera" . Retrieved 24 September 2009.
  28. ↑ 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.
  29. ↑ Visual Molecular Dynamics license
  30. ↑ 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.
  31. ↑ "VMD - Visual Molecular Dynamics" . Retrieved 24 September 2009.
  32. ↑ "WHAT IF homepage" . Retrieved 24 September 2009.
  33. ↑ "YASARA – Yet Another Scientific Artificial Reality Application" . Retrieved 24 September 2009.
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