Welcome to ChemMapper

ChemMapper is a free web server for computational drug discovery based on the concept that compounds sharing high 3D similarities may have relatively similar target association profile. ChemMapper integrates nearly 300 000 chemical structures from various sources with pharmacology annotations and over 3 000 000 compounds from commercial and public chemical catalogues. In-house SHAFTS method which combines the strength of molecular shape superposition and chemical feature matching is used in ChemMapper to perform the 3D similarity searching, ranking, and superposition. Taking the user-provided chemical structure as the query, SHAFTS aligns each target compound in the database onto the query and calculates the 3D similarity scores and the top most similar structures are returned. Base on these top most similar structures whose pharmacology annotation is available, a chemical-protein network is constructed and a random walk algorithm is taken to compute the probabilities of the interaction between the query structure and proteins which associated with hit compounds. These potential protein targets ranked by the standard score of the probabilities. ChemMapper can be useful in a variety of polypharmacology, drug repurposing, chemical-target association, virtual screening, and scaffold hopping studies.

To use ChemMapper, simply draw a chemical structure in the JSME window below (or upload a file containing single molecular information in SMI, SDF, or MOL2 format) and Click "Submit". To view the result, here is an Example of polypharmacology effect of the marketed selective HIV Reverse transcriptase inhibitor Rescriptor, which were experimentally found to be binding Histamine H4 receptor (doi:10.1038/nature08506) and predicted successfully by ChemMapper (rank 6). For detail information of ChemMapper, please follow the instructions in the Documentation.

Please do not submit more than 10 jobs once.

Job Submission

Input Molecule

Sketch your molecule and

Input SMILES help

Or Upload a molecule file in smi, sdf and mol2

Job information

1.The query molecule can only contain organic elements like C, O, N, P, S, H, and halogen!
2.The query molecule cannot have more than 50 heavy atoms to reduce the computation cost.

Options for ChemMapper

3D similarity method



2D similarity method



Bioactivity Databasehelp

KEGG (5,928)help

PDB (7,072)help

Compound Databasehelp

Upload a Databasehelp

Note: File size must less than 10MB!

Similarity Thresholdhelp

Already had a job ID? Check the result now!

ChemMapper may NOT be used for commercial purposes.


If you use ChemMapper, Please cite:

ChemMapper is Powered by:

ChEMBL bindingDB DrugBank PDB
JSME OpenBabel ChemAxon Jmol

If you have problems, please contact us: lilab_ecust@163.com

Last update: 30th Dec. 2016

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