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New Search Engine Software Enables Scientists to Identify Molecules by Shapes

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Scientists at the National Foundation for Cancer Research (NFCR) Center for Computational Drug Discovery at the University of Oxford unveiled that they have developed a 3D Molecule Search Engine that is up to 14,000 times faster than previously developed similar search engine technology.

Known as Ultrafast Shape Recognition (USR), the searching system can create an accurate mathematical picture for the shape of any chemical compounds and allows molecules with similar shapes to be sought out quickly from Oxford’s database of 3.5 billion molecule structures.

Researchers at the NFCR Center for Computational Drug Discovery believe this shape-oriented searching system has enormous potential for medical research and new drug development because it increases the efficiency of virtual screening technology, reduces the need for expensive biological tests and tackles the high failure rate currently faced by the pharmaceutical industry.

“This new search capability enables us to find drug-like molecules within a huge database in a few hours rather than a few years,” said Dr. Pedro Ballester of Oxford’s Department of Chemistry who led the research with Professor Graham Richards, Director of the NFCR Center for Computational Drug Discovery.

Virtual screening is widely used for new drug development. It screens for compounds that most closely resemble a drug or a drug-like molecule to provide novel drug leads.

The 3D molecular shape comparison is a key technology to carry out the virtual screening. However, the efficiency of current comparison technology is not high enough to do the job, especially in dealing with large databases.

USR is based on “moments of distance distributions” of the molecules and eliminates the need for molecule alignment to do the comparison. It works like comparing the relative position of a person’s features to identify his/her face – and it works regardless of how the molecules are oriented.

“There is no speed limit on the way to find new anticancer drugs. The ultrafast speed provided by USR method in searching for novel drug leads will bring significant benefits not only to cancer research, but to other areas of medical research as well,” said Dr. Michael Wang, Vice President of Science with the National Foundation for Cancer Research.