University of York - Department of Computer Science

AURAmol home page

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:


This is the home page of AURAmol, the technology that allows a user to take a candidate 2D or 3D molecular shape and use it to search for similarly shaped molecules in large databases. The system was developed in the Computer Science Department, University of York, UK in collaboration with Cybula Ltd. It is generally used for searching through databases of complex small molecules with size in the order of 60 atoms. Extensions to the basic method allow the system to take into account local properties of the molecules. AURAmol is part of the AURA high performance pattern recognition technology that Cybula has developed to solve a wide range of similarity-based search problems.

Principal features of the technology are:


The AURAmol system describes the molecule as a set of points in space. These points are joined in a graph that is then used to search the database of molecules. The nodes in the graph contain attributes that describe the local properties of the molecule at that point. The match engine is composed of a number of discrete knowledge-containing units working together through a process known as constraint propagation. The procedure efficiently searches large databases for potential matches. Matches are then returned in the form of a set of molecules, ranked by similarities to the query molecule.


The AURAmol system has been developed in cooperation with the University of York, Computer Science Department, UK in association with a number of biotech companies.

Using AURAmol

The AURAmol system may be embedded into many applications. The system exists as a C++ library and runs on Linux, Windows and UNIX-like platforms. The system can be run on small PCs to supercomputers.

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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