This is a list of notable software systems that are used for visualizing macromolecules.[1]
Name | Data | License | Technology | Citations | Comments |
---|---|---|---|---|---|
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. | |
Molden | MM XRD | Proprietary, free use academic | [12] | ||
Molecular Operating Environment (MOE) | HM MD MM NA QM SMI XRD | 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 XRD | Free open-source | Java 3D applet or standalone program | ||
Ovito | MM XRD EM MD | Free open-source | Python | [13][14] | |
PyMOL | MM XRD SMI EM | Open-source[15] | Python | [16][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 | [17][18][19][self-published source?] | ||
SAMSON | MM MD SMI MRI | Proprietary, limited free version | Windows, Linux, Mac. C++ (Qt) | [20] | 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[21] | Standalone program | [22] | Edit, visualize and run simulations on various molecular systems. |
Spartan | MM QM | Proprietary[23] | Standalone program | [24] | 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[25] for noncommercial use[26] | Python | [27][28][self-published source?] | Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[29] |
VMD | EM MD MM | Free open-source for noncommercial use[30] | C++ | [31][32][self-published source?] | |
WHAT IF | HM XRD | Proprietary, shareware for academics | Fortran, C, OpenGL, standalone | [33][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 | [34][self-published source?] | Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface. |
The tables below indicate which types of data can be visualized in each system: