Downloadable Molecular Graphics Tools
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Program Type
| Program | Description | License | Input | Output |
|---|---|---|---|---|
 PyMOL | Molecular visualization system that can produce high-quality 3D images of small molecules and biological macromolecules. | Open Source | – Molecular Structures – Trajectories & Topologies – Volumetric Data – Geometry – Scripts – Annotated Structures | – Molecular Structures – Volumetric Data – Geometry – Images |
 Jmol | Java viewer for chemical structures in 3D with features for chemicals, crystals, materials, and biomolecules. | Open Source | – Molecular Structures – Trajectories & Topologies – Spectral Data – Crystallographic Data – Quantum Chemistry Data – Scripts – State Files | – Molecular Structures – Images – Animations – Vector Graphics – Session State Scripts |
 UCSF Chimera | A highly extensible program for interactive visualization and analysis of molecular structures and related data. | Free for academic use | – Molecular Structures – Sequences – Density Maps – Trajectories & Topologies – Alignment Files – Script Files | – Molecular Structures – Images – Session Files – Movie Files – 3D models – Export for 3D Printing (STL) |
 VMD | Designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies. | Free for non-commercial use | – Molecular Structures – Trajectories & Topologies – Volumetric Data – Simulation Data – Scripts | – Molecular Structures – Images – Movies – VRML/X3D |
 Coot | Crystallographic Object-Oriented Toolkit, a software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. | GNU GPL | – Crystallographic Data – Electron Density Maps – Molecular Structures – Sequence Data | – Molecular Models – Maps – Images |
 Swiss-PdbViewer (DeepView) | A tool for protein structure analysis, with capabilities for aligning, superposing, and analyzing proteins. | Free | – Molecular Structures – Trajectories & Topologies | – Images – PDB Files |
 Avogadro | Advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | GPL | – Molecular Structures – 3D Coordinates – Crystallographic Data Files – Various Chemical File Formats | – Molecular Structures – Images – XYZ Files – PDB Files |
| NGL Viewer | Interactive tool for molecular visualization, primarily of large biomolecular complexes. | Open Source | – PDB Files – Molecular Formats | – Molecular Structures |
 MOE (Molecular Operating Environment) | Integrates visualization, simulation, and modeling of small molecules and biological systems. | Commercial | – Molecular Structures – Ligands and Receptors – Chemical Properties – Biological Sequences | – Molecular Structures – Docking Results – Images |
 AutoDock | Suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | GNU GPL | – Ligand Structures – Receptor Structures – Grid Maps – Config Files | – Docking Log Files – Docking Poses |
 YASARA | Molecular graphics, modeling and simulation program used for a wide range of scientific research, including drug design and protein engineering. | Freemium | – Molecular Structures – Density Maps – Trajectories & Topologies | – Molecular Structures – Images – Movies – Simulation Data |
 Schrodinger Suite | Integrated suite for computational chemistry, molecular modeling, and bioinformatics, widely used in pharmaceutical research. | Commercial | – Molecular Structures – Ligands and Receptors – Biological Sequences | – Molecular Structures – Images – Reports |
 MarvinSketch | Chemical editor for drawing chemical structures, queries, and reactions. It is used by chemists for creating publication-quality drawings. | Commercial | – 2D Chemical Drawings – Query Structures – Reactions | – Chemical Structures – Images – Reaction Schemes |
| Mol* Viewer | ||||
 Amira | Powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding Life Science and bio-medical data coming from all types of sources. | Commercial | – 3D Image Data – Molecular Data – Tomography Data – Microscopy Data | – Visualizations – Animations – Images – VRML/X3D |
 Biovia Discovery Studio | A comprehensive suite for molecular modeling, simulation, and visualization, particularly popular in drug design and materials science. | Commercial | – Molecular Structures – Biological Sequences – Chemical Properties | – Molecular Structures – Images – Animations |
 Rosetta | A software suite including algorithms for protein structure prediction, design, and docking. | Free for academic use | – Sequence Data – Structure Data – Experimental Constraints | – Protein Models – Docking Solutions |
 NAMD | High-performance parallel molecular dynamics code for large-scale biomolecular systems simulation. | UIUC/NCSA Open Source License | – Molecular Structures – Trajectories & Topologies | – Molecular Dynamics Trajectories |
 GROMACS | A versatile package to perform molecular dynamics, i.e., simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | GNU GPL | – Molecular Structures – Trajectories & Topologies – Force Fields | – Simulation Data – Energy Information |
 Gaussian + GaussView | Provides state-of-the-art capabilities for electronic structure modeling, GaussView is the graphical interface. | Commercial | – Electronic Structures – Quantum Chemical Data | – Molecular Orbitals – Charge Distributions |