I recently came across a nice tool for depicting multiple molecules called CDK Depict (thanks to Ruben for sending it to me), so I decided to explore what other web-based molecule visualization and drawing tools are available.
- Very straightforward and easy-to-use tool for molecule drawing (or drawing from formats such as SMILES, SMARTS and InChI)
- Various export options for structures and images
- Lacks some of the sophisticated functionality of some of the other tools but does the job for simple tasks
- Owned by the RSC and allows you to draw molecules and search the ChemSpider database (containing >100 million structures) by searching for exact matches or performing similarity or substructure search)
- Can easily convert the structures from another format (e.g. name, SMILES, InChI) or load it from a structure or image file
- Uses JSME and JSmol for visualising molecules in both 2D and 3D
- Has a few options for customizing the 3D rendering (e.g. ball and stick vs spheres, colour, element labels)
- Can perform optimization of the structure in 3D
- CDK Depict allows you to visualize (rather than draw) multiple molecules from SMILES strings or an sdf
- The interface is really easy to use and has various drawing options for modifying colour, annotation, hydrogens and whether to abbreviate groups and reagents
- Individual images can be easily downloaded as SVG, PNG or PDF files
- It can also be used to depict reactions
- MolView is a really nice tool that allows you to draw and visualize molecules in both 2D and 3D
- Can also be used for visualizing macromolecules
- You can easily search for and view molecules in databases such as PubChem and the PDB
- The tools tab allows you to see calculated properties and spectroscopy data
- Many different export options exist, including mol, PDB and CIF file formats (in addition to image files)
- Overall a powerful tool with lots of additional functionality not listed here!
These are just a few examples and I am sure there are many more that I have missed off the list!
