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 | [2] | Windows, Linux, Mac | [3] | Based on OpenInventor/OpenGL; focusing on life and biomedical sciences. |
Ascalaph Designer | MM MD QM | C++ | [4] | Graphics, model building, molecular mechanics, quantum chemistry. | |
Avizo | EM MM MRI Optical SMI XRD | [5] | Windows, Linux, Mac | [6] | Avizo is derived from Amira and focusing on materials science. |
Avogadro | MM XRD MD | open-source, GPL | C++, Qt, extensible via Python modules | ||
BALL | Molecular dynamics MM NMR | LGPL open-source | Standalone program | [7] | |
Cn3D | open-source | Standalone program | [8] | In the NCBI C++ toolkit | |
Coot | XRD | open-source | |||
Gabedit | XRD MM | open-source | C | [9] | |
Jmol | open-source | Java (applet or standalone program) Transpiled HTML5/JavaScript for browser | [10] | Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry | |
MDL Chime | , free use noncommercial | C++ browser plugin for Windows only | [11] | 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 | open-source (MIT) | TypeScript (WebGL, React) | [12] | Viewer currently used by RCSB-PDB and EMBL/PDBe. Contains a scripting language. |
Molden | MM XRD | , free use academic | [13] | ||
Molecular Operating Environment (MOE) | HM MD MM NA QM SMI XRD | 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 | open-source | Java 3D applet or standalone program | ||
PyMOL | MM XRD SMI EM | Open-source[14] | Python | [15] | According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL. |
RasMol | open-source | C standalone program | [16] [17] [18] | ||
SAMSON | , limited free version | Windows, Linux, Mac. C++ (Qt) | [19] | Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements. | |
Sirius | open-source | Java 3D applet or standalone program | No longer supported as of 2011. | ||
Scigress | MM QM | [20] | Standalone program | [21] | Edit, visualize and run simulations on various molecular systems. |
Spartan | MM QM | [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 | open-source[24] for noncommercial use[25] | Python | [26] [27] | Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[28] |
VMD | EM MD MM | open-source for noncommercial use[29] | C++ | [30] [31] | |
WHAT IF | HM XRD | , shareware for academics | Fortran, C, OpenGL, standalone | [32] | 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 | , limited free version | C-assembly, Windows, Linux, Mac | [33] | 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: