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 | ||
Mol* (Molstar) | Free open-source | Web-based; uses WebGL and TypeScript | [13] | Integrated into RCSB and PDBe websites | |
PyMOL | MM XRD SMI EM | Open-source [14] | Python | [15] [ self-published source? ] | |
RasMol | Free open-source | C standalone program | [16] [17] [18] [ self-published source? ] | ||
SAMSON | MM MD SMI MRI | Proprietary, limited free version | Windows, 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? ] | |
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. |
The tables below indicate which types of data can be visualized in each system: