OpenEye Releases FastROCS 1.0 – Extremely Fast 3D Molecular Shape Comparison on NVIDIA Tesla GPUs

SANTA FE, N.M.--(BUSINESS WIRE)-- OpenEye Scientific Software, Inc. (, the developer of innovative molecular modeling and cheminformatics solutions for drug discovery, recently released FastROCS 1.0 to its collaborators at Abbott Labs and Pfizer. FastROCS is an extremely fast shape comparison application that leverages the parallel processing capabilities of NVIDIA Tesla GPUs to enable real-time shape similarity for virtual screening, lead hopping and shape clustering.

Dr. Anthony Nicholls, CEO and President of OpenEye, had the following to say, “In my career, I've been fortunate enough to have witnessed firsthand the game-changing effects that dramatic speed improvements can have on a technology -- there is something special about speed-ups of a hundred or more which always seems to spawn new and unexpected areas of application as well as enhancing the original function. OpenEye is already the industry leader in shape similarity having established a gold standard with ROCS; however, we now stand at the forefront of a revolution in the use of shape similarity as a result of FastROCS. There are many obvious new uses for FastROCS, such as library clustering, that were previously difficult and time-consuming that now will be trivial, but I am particularly keen to see to what other unexpected tasks we and others will now apply this well-validated approach.”

Molecular similarity based on 3D shape comparison has become the industry standard over the past decade because it is one of the most accurate predictors of shared bioactivity. The technology underlying FastROCS is based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. Ligand based shape similarity has repeatedly proven itself to be an extremely powerful tool in the drug discovery process and has been shown to be competitive and frequently superior to structure based approaches both in terms of overall performance and in consistency.

Leveraging the CUDA parallel processing architecture of NVIDIA GPUs, FastROCS is capable of matching over 2 million conformations per second, which means that corporate collections can be searched in seconds instead of hours or days.

Brian Cole, the lead developer behind FastROCS, states that “Corporate collections of molecules are vast, often with more than 100 million conformations in many cases. FastROCS running on a single computer equipped with four of the latest generation NVIDIA Tesla GPUs to analyze these collections can achieve performance increases that are multiple orders of magnitude greater than one might see with traditional hardware.”

Andrew Cresci, general manager of vertical solutions at NVIDIA, states that “FastROCS is an important milestone in drug discovery and will open new avenues of research with the incredible performance achieved by their aggressive use of NVIDIA GPUs.”

In addition to virtual screening and shape-based clustering, FastROCS alignments have a number of potential applications including:

  • 3D QSAR
  • SAR analysis
  • Understanding of scaffold diversity
  • Detection of common binding elements

FastROCS has already been recognized for its superior performance on the GPU having won the first annual “Khronos OpenCL OCL Award” in the category of “Best Performance” at the SuperComputing 2010 meeting in New Orleans this past November.

Dr. Bob Tolbert, Vice President of Development, will be presenting a talk on FastROCS titled "FastROCS: Revolutionizing Drug Discovery on the GPU" on April 13th at the upcoming Bio-IT World meeting in Boston. Individual demonstrations will be available at the OpenEye booth in the main exhibition hall.


OpenEye Scientific Software, Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg, France and Tokyo, Japan. It was founded in 1997 to develop large-scale molecular modeling applications and toolkits. Primarily aimed towards drug discovery and design, areas of application include:

The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors and runs on Linux, Windows, and Mac OS X. For further information on the company and its products, see


OpenEye Scientific Software, Inc.
Joseph Corkery, M.D.
Vice President, Business Development
+1 505-473-7385 x76
[email protected]

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