Tools
Smi2Depict
Generate 2D images from SMILES.
Babel
Convert between molecule file formats.
Reaction Processor
Generate product libraries.
Pattern Match Counter
Count functional groups (sub-structures).
Pattern Count Screen
Screen molecules by functional group count.
MSFragment
Fragment molecules for mass spec analysis.
Mass2Structure
Search ChemDB by monoisotopic mass and substructure filtering.
Protein Target Predictor
Predict activities of small molecules against a large set of protein targets
Datasets
Chemical datasets
Datasets for training and testing machine learning and other algorithms.
Chemical Reactivities datasets
Dataset of chemical reactivities
Publications
Publications
Relevant scientific articles published by our team.

Miller R.J., Dashuta A.E., Rudisill B., Van Vranken D., Baldi P. Mechanism-Aware Deep Learning for Polar Reaction Prediction Journal of American Chemical Society, 2025, Oct 2025

Tavakoli M., Miller R.J., Angel M.C., Pfeiffer M.A., Gutman E.S., Mood A.D., Van Vranken D., Baldi P. PMechDB: A Public Database of Elementary Polar Reaction Steps Journal of Chemical Information and Modeling, 64 (4), Mar 2024

Tavakoli M., Baldi P., Carlton A.M., Chiu Y.T., Shmakov A., Van Vranken D. AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning NeurIPS Proceedings 36 (NeurIPS 2023), 2023

Tavakoli M., Chiu Y.T.,Baldi P.,Carlton A.M., Van Vranken D., RMechDB: A Public Database of Elementary Radical Reaction Steps, Journal of Chemical Information and Modeling, 63 (4), Feb 2023

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).
Molecules
ChemicalSearch
Find a molecule by its name, structure, or similarity to another molecule and filter the results.
Virtual Chemical Space
Interactively deconstruct a target molecule into possible chemical precursors and reassemble them into a combinatorial library of real or virtual molecules around the target.
MOLpro
Calculate or predict molecular properties other than 3D structure.
AquaSol
Predict aqueous solubility of small molecules using deep learning and ensembles.
COSMOS (downloadable)
Predict 3D molecular structures using open crystallography libraries.
COSMOS
Predict 3D molecular structures.
RNN Tool-Kits for Predicting Molecular Properties from SMILES
Inner- and Outer Recursive Neural Networks for Chemoinformatics
Reactions
PMechRP
Polar Mechanistic Reaction Predictor

PMechDB
Polar Mechanistic Reaction Database:
PMechDB is a live platform for aggregating, curating, and distributing chemical reactions in the form of polar elementary steps to accelerate research in chemoinformatics and polar reaction modeling. The PMechDB platform is designed to facilitate training deep learning and other AI models in data-driven workflows using its tabular data, with no need for additional pre-processing steps. It provides a unified model that ought to facilitate data sharing, model building, dissemination, and publications. We encourage the community to explore and use the PMechDB data and functionalities, and contribute to its expansion.
RMechRP
Radical Mechanistic Reaction Predictor

RMechDB
Radical Mechanistic Reaction Database:
RMechDB is a live platform for aggregating, curating, and distributing chemical reactions in the form of elementary radical steps to accelerate research in chemoinformatics and radical reaction modeling.
Reaction Predictor
Predict reaction outcomes and mechanisms using machine learning.
Reaction Explorer
Learn and practice reactions, syntheses, and mechanisms interactively with support for: automated generation of problems, curved-arrow mechanism diagrams, and inquiry-based learning.
Reaction Predictor (older version)
Previous system to predict reaction outcomes and mechanisms using machine learning.
ReactionMap
Predict the mapping of reactant atoms to product atoms for chemical reactions.
Download & Documentation
Download
Download entire set of chemical isomers contained within ChemDB.
Implementation
System implementation materials such as the database schema with data definition and source / vendor information table.
Analysis
Data analysis tables and charts based upon ChemDB contents.
Acknowledgements
OpenEye Scientific Software
Provider of software tools and components, including OEChem, Ogham and LexiChem.
ChemAxon
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.
Chemical Vendors
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.