Neurosnap Molecular Explorer

Explore proteins, nucleic acids, ligands, density maps, and molecular trajectories in your browser with the Neurosnap Molecular Explorer, powered by Mol* (MolStar). Load multiple files as overlays, inspect binding sites and disulfide bonds, measure molecular geometry, screen structure quality, view AlphaFold confidence and custom scores, and export images or sessions. Supports PDB, mmCIF/BCIF, PQR, SDF/MOL/MOL2, GRO, CCP4/MRC maps, Gaussian CUBE fields, and coordinate trajectories. Uploaded files stay on your device.


Open your files

Use the viewer’s Open file control, drag files into the viewer, or select them below. Select multiple structures to overlay them; the last structure becomes active. Uploaded files are processed in your browser and stay on your device.

Supported structures: PDB, PQR, mmCIF/BCIF, SDF, MOL, MOL2, and GRO, including gzip files. Load CCP4/MRC/MAP density maps or Gaussian CUBE fields alongside structures. For DCD, XTC, TRR, or NetCDF trajectories, select one coordinate-bearing topology file together with one trajectory file. Multi-model structures also support frame selection and playback.

Examples & demos

Choose a demo to explore a scene, or use Quality screen to inspect the currently active structure. The density, orbital, and MOL2 ligand examples are synthetic fixtures rather than experimental or calculated results.

Explore and analyze

Use the structure controls to choose the active model and toggle overlay visibility. Select atoms or residues in the viewport or sequence, change representations and colors, inspect interactions, and measure distances, angles, or dihedrals. Density controls adjust map surfaces independently of the structures.

More opens AlphaFold confidence, PAE, measurement, and export options. Use confidence coloring only for predicted structures with pLDDT scores; experimental B-factors are not prediction confidence. Export a molecular image or save a session to retain the scene and its settings.


Citation

If you've found this tool to be useful, please consider citing us as seen below.


David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose, Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, Volume 49, Issue W1, 2 July 2021, Pages W431–W437, https://doi.org/10.1093/nar/gkab314

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/


Frequently Asked Questions

For additional questions, please feel free to contact us here.