NP-Scout: quantification and visualization of NP-likeness


NP-Scout is a free web service that for the NP-Scout utilizes random forest classifiers trained on more than 161k natural products and an equal number of synthetic molecules.


Molecular structures are loaded either by directly drawing a molecule with the JSME Molecular editor [1], by pasting a SMILES into the field “Enter SMILES”, or by uploading a text file containing a list of SMILES. NP-Scout runs a thorough data preparation protocol to standardize the input. Therefore, chemical structures do not need to be preprocessed by the user with respect to hydrogen annotation, aromatization, protonation, tautomerism and stereochemistry. Salts are also recognized, and the minor components removed prior to calculations. [1] Bienfait, B.; Ertl, P. JSME: a free molecule editor in JavaScript. J. Cheminform. 2013, 5, 24.

Example upload file

Lists of SMILES should be formatted as shown in the following examples: Example 1: One SMILES per row with no additional data C=C1C(=O)OC2C1CCC1(C)OC13CC=C(C)C23
CC12C=CC(=O)NC1CCC1C2CCC2(C)C(C(=O)Nc3cc(C(F)(F)F)ccc3C(F)(F)F)CCC12 Example 2: One SMILES per row with additional data C=C1C(=O)OC2C1CCC1(C)OC13CC=C(C)C23 arglabin
CC12C=CC(=O)NC1CCC1C2CCC2(C)C(C(=O)Nc3cc(C(F)(F)F)ccc3C(F)(F)F)CCC12 dutaseride The following separators may be used: " " (space character), "\t" (tab), ";" or ",".

Running the calculations

Calculations are started by clicking the “Submit” button. A new web page will load that reports on the progress of calculations and displays a web link that allows users to return and inspect the results once all calculations have been completed.

Analyzing results

The results page mainly consists of a table which presents the predictions for the query molecules. The results in .csv format and a log file can be downloaded for further use. Errors and warnings are listed in the .log file and the .csv file contains the table of results except the similarity maps.
SMILES Molecule name Error/Warning NP class probability Similarity maps