University of York - Department of Computer Science

AURAmol search tips

Searches can be launched from any page on this website via the search box, (shown below, with a blue background). The are several ways to run searches using AURAmol. If you do not have a molecule file to hand, then you can use a molecule from our database to experience a search. The simplest way to do this to take Option 1: click on the "Random Molecule" button and a molecule from the database will be chosen for you at random, and resulting matches displayed. Alternatively, you can look for a specific molecule by entering its index in the box for Option 2.

Option 3 allows you to upload a molecule and retrieve similar matches from the database. Note that the database we use contains molecules of the order of 60 atoms. Molecules with significantly larger or smaller number of atoms are unlikely to return any (good) matches. Finally, the minimum match score for the first stage of the matching process can be set by selecting from the range of percentages in the drop down menu marked Threshold.

Option 1- Select a random molecule from our database:
Option 2- Specify any molecule from 0 to 999 from our database:
Option 3- Upload a molecule file:

Interpreting the results

If any matches are found, they will be displayed below the search box. The first three results from a typical search are shown below. The search engine returns at most 20 matches. There are five columns in the search results table. The first column gives the ranking of the match. The second column gives the score for the match as a percentage. The third column gives the index of the molecule in the database. The fourth column shows the SMILES string for the match. Finally, the fifth column contains a button which launches a small popup window for viewing the query and matched molecules.


Search on molecule 678 returned 299 matches with a threshold of 65%

199.0-100.0678 c1c(ccc(c1­)F)Nc1scc(­n1)c1ccncc­1
285.7985 c1c(ccc(c1­)F)c1nc(sc­1)Nc1ccc(c­c1)F
385.711168 c1c(ccc(c1­)Cl)c1sc(n­c1)Nc1ccc(­cc1)F


What database are the searches carried out on?

We have been given permission to use a small subset of the ZINC molecular database. Zinc is a freely available database of molecules for virtual screening.

How are the molecules displayed?

On this website, molecules are displayed using the jMol applet, but AURAmol is not tied to any particular display format.

What molecule formats can I upload?

This web service uses OpenBabel to translate a wide range of molecule files into a format that AURAmol can understand.

Cybula Ltd Contact: Aaron Turner, ACAG, Department of Computer Science,
the University of York, Heslington, York YO1 5GH, UK
tel. +44 (0)1904 325630
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