Generate 2D images from SMILES.

Convert between molecule file formats.

Generate product libraries.

Count functional groups (sub-structures).

Screen molecules by functional group count.

Fragment molecules for mass spec analysis.

Search ChemDB by monoisotopic mass and substructure filtering.

Predict activities of small molecules against a large set of protein targets
Datasets for training and testing machine learning and other algorithms.
Relevant scientific articles published by our team.
If you use any data or tools from the ChemDB Portal, please cite the following article:
Chen, J. H., Linstead, E., Swamidass, S. J., Wang, D. & Baldi, P. ChemDB update-full-text search and virtual chemical space. Bioinformatics 23, 2348-2351 (2007).
Find a molecule by its name, structure, or similarity to another molecule and filter the results.

Interactively deconstruct a target molecule into possible chemical precursors and reassemble them into a combinatorial library of real or virtual molecules around the target.

Calculate or predict molecular properties other than 3D structure.

Predict aqueous solubility of small molecules using deep learning and ensembles.

Predict 3D molecular structures using open crystallography libraries.
Predict 3D molecular structures.

Inner- and Outer Recursive Neural Networks for Chemoinformatics
Learn and practice reactions, syntheses, and mechanisms interactively with support for: automated generation of problems, curved-arrow mechanism diagrams, and inquiry-based learning.

Predict reaction outcomes and mechanisms using machine learning.

Predict the mapping of reactant atoms to product atoms for chemical reactions.
Download & Documentation
Download entire set of chemical isomers contained within ChemDB.
System implementation materials such as the database schema with data definition and source / vendor information table.
Data analysis tables and charts based upon ChemDB contents.
Provider of software tools and components, including OEChem, Ogham and LexiChem.
Molecular visualization applet, including 3D views and mechanism arrow diagram sketching.

JME Editor (Peter Ertl, Novartis)
Molecule editing Java Applet to enable sketching of your own reactants.
All of the vendors who have supplied their chemical information catalogs that comprise the core data beneath ChemDB. The source information table includes a complete listing.