webMolCS: Visualizing Molecules in 3D Chemical Space

Fingerprint Sim map PCA map
Atom Pair Fingerprint (APfp)
SMILES Fingerprint (SMIfp)
Molecular Quantum Number (MQN)
Pharmacophore Extended Atom Pair Fingerprint (Xfp)
Daylight Type Substructure Fingerprint (Sfp)
Circular Extended Connectivity Fingerprint (ECfp4)
MinHash Fingerprint (MHFP6)

*1) Approximate time is shown (as button label) for calculation of map for 1000 compounds.

*2) To generate the map for your set: input the compound list in the below text box and hit a button (corresponding to a fingerprint and a method of your choice) in the above table.

*3) Click here for Help page

Input: SMILES+" "+Name of molecule+" "+Value for color code (optional)+" "+Satellite option (1 or 0, optional, max. 50 Satellites)

Example: C1CCCCC1 test

Example: C1CCCCC1 test 0.2

Input up to 5000 molecules. The first molecule in the list is used as reference for similarity sorting. Simply copy-paste your input in below text box or select the file using Choose file button.

Clear List

webMolCS: Demo Examples from Publications

1) WebMolCS: a Web-Based Interface for Visualizing Molecules in 3D Chemical Spaces Mahendra Awale, Daniel Probst and Jean-Louis Reymond, J. Chem. Inf. Model., 2017, 57(4), 643–649.

Fingerprint Sim map
(A)		 PCA map
(A)		 Sim map
(B)		 PCA map
(B)		 Sim map
(C)		 PCA map
(C)		 Sim map
(D)		 PCA map
(D)
Atom Pair Fingerprint (APfp)
SMILES Fingerprint (SMIfp)
Molecular Quantum Number (MQN)
Pharmacophore Extended Atom Pair Fingerprint (Xfp)
Daylight Type Substructure Fingerprint (Sfp)
Circular Extended Connectivity FIngerprint (ECfp4)

Set A: 5000 nearest neighbors of nicotine extracted from GDB-13. Click here for input file.

Set B: 1503 Aurora A kinase inhibitors from ChEMBL. Click here for input file.

Set C: 48 Aurora A Kinase Inhibitors reported from our group. Click here for input file.

Set D: 197 compounds active against three different targets. 100 compounds for Focal adhesion kinase 1 (fak1), 56 compounds for Thymidine kinase (kith) and 41 compounds for Catechol O-methyltransferase (comt). Compounds were extracted from eDUD database. Click here for input file.

To access the 3D-map click on a button (corresponding to set, fingerprint and method of your choice) in the above table.

2) ChEMBL-Likeness Score and Database GDBChembl, Sven Bühlmann and Jean-Louis Reymond, Frontiers in Medicinal Chemistry, 2020

Description of Map Xfp Sim map
Figure 3g,h. MQN nearest neighbors of nicotine from GDBChEMBL, FDB17 and GDBMedChem.

3) Optimizing TRPM4 inhibitors in the MHFP6 chemical space, Clémence Delalande, Mahendra Awale, Matthias Rubin, Daniel Probst, Lijo C. Ozhathil, Jürg Gertsch, Hugues Abriel and Jean-Louis Reymond, European Journal of Medicinal Chemistry, 2019

Description of Map MHFP6 Sim map
Figure 2. MHFP6 chemical space map of initial screening set leading to CBA. Main map: map color-coded by activity (blue=inactive, red=most active)
Figure 4. MHFP6 chemical space map of the overall SAR of TRPM4 analogs. Main map: map color-coded by activity (blue=inactive, red=most active)
Figure 5. Visualization of benchmarking sets from DUD-E using MHFP6 similarity maps in WebMolCS, color coded as actives (red) or decoys (blue)
Figure 5a. Thymidine kinase (kith)
Figure 5b. catechol O-methyl transferase (comt)
Figure 5c. focal adhesion kinase 1 (fak1)
Figure 5d. farnesyl diphosphate synthase (fpps)
Figure 6. Visualization of active sets from DUD-E in combination with approved drugs from DrugBank using MHFP6 similarity maps in WebMolCS, color coded by set (actual value option in controls).
Figure 6a. green: Fak1 (focal adhesion kinase 1), red: kith (thymidine kinase), blue: DrugBank.
Figure 6b. green: kith (thymidine kinase), red: fpps (farnesyl diphosphate synthase), cyan: Fak1 (focal adhesion kinase 1), blue: DrugBank
Figure 6c. green: kith (thymidine kinase), red: comt (catechol O-methyl transferase), cyan: Fak1 (focal adhesion kinase 1), blue: DrugBank
Figure 6d. green: kith (thymidine kinase), red: fpps (farnesyl diphosphate synthase), cyan: Fak1 (focal adhesion kinase 1), yellow: comt (catechol O-methyl transferase), blue: DrugBank

4) Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT‐β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2 Marion Poirier, Mahendra Awale, Matthias A. Roelli, Guy T. Giuffredi, Lars Ruddigkeit, Lasse Evensen, Amandine Stooss, Serafina Calarco, James B. Lorens, Roch‐Philippe Charles, Jean‐Louis Reymond, ChemMedChem, 2018, doi:10.1002/cmdc.201800554

Description of Map Xfp Sim map
Figure 5. 3D‐similarity map of triazines 1–18 (red spheres) and nearest neighbors of 1 from ChEMBL annotated as LPAAT‐β (cyan), A2aR (blue) or VEGFR‐2 (yellow) inhibitors.

5) Identification of potent and selective small molecule inhibitors of the cation channel TRPM4 Lijo Cherian Ozhathil, Clémence Delalande, Beatrice Bianchi, Gabor Nemeth, Sven Kappel, Urs Thomet, Daniela Ross‐Kaschitza, Céline Simonin, Matthias Rubin, Jürg Gertsch Martin Lochner, Christine Peinelt, Jean‐Louis Reymond, and Hugues Abriel, Br. J. Pharmacol., 2018, doi:10.1111/bph.14220

Description of Map Sfp Sim map
Figure 8. Chemical space analysis. Selected view of an interactive 3D map of substructure fingerprint similarity representing each of the 470 compounds tested as one sphere. The map is colour‐coded by pIC50 value from blue (lowest value) to red (highest value).