SBI-Moldyn Awarded U.S. Technology Patent.

Business Editors and Health/Medical Writers

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SAN DIEGO--(BW HealthWire)--Jan. 19, 2001

A Subsidiary of Structural Bioinformatics Inc. (SBI)

Accelerates the Worldwide Trend Towards Broad Use of Structural

Proteomics

Privately-held Structural Bioinformatics Inc. (SBI), a recognized leader in computational proteomics and 3-D protein structure determination, today announced that it has been awarded U.S. patent coverage on the latest innovative technology for generating 3-D protein structures.

This technology was developed by SBI-Moldyn, the recently acquired subsidiary of SBI located in Cambridge, Mass. This patent, U.S. Pat. No. 6,125,235, is an important addition to SBI's growing array of rapid and yet highly accurate methods for providing the proteomics and drug discovery world with the best 3-D protein structures "on demand."

The invention known as ASTER-N (Automated STructure Estimation and Refinement for NMR) employs SBI-Moldyn's innovative and unique Nonlinear Recursive Filter (NRF) for the super-fast computer generation of 3-D structures of large proteins. The NRF recursively processes experimental data (e.g., NMR NOE intensities) to simultaneously produce a refined structure (coordinate set) and a quantitative measure of accuracy (a covariance matrix) for each protein structure. NMR refinement tests, conducted with the NRF on a variety of proteins, consistently demonstrate computational speed improvements of more than two orders of magnitude compared to conventional methods (e.g., simulated annealing) with equal or better accuracy. These tests also reveal the ability to rapidly converge on the optimum refined structure even if the starting structure is far from the most favorable (i.e., a much wider radius of convergence).

The practical efficiency of the NRF for very large protein structures is achieved via a technique called Refinement Wave processing, which is also part of the subject patent. Refinement Wave processing makes it possible to break down a large-scale structure determination problem into a sequence of smaller interconnected problems. In addition, ASTER-N's computational speed and recursive filtering strategy offer an attractive basis for automating and dramatically speeding-up the most severely rate-limiting and laborious step in structure generation by NMR, the NOE peak assignment problem.

ASTER-N is currently in beta testing at a number of research laboratories. The development of ASTER-N was partly supported by a Small Business Innovative Research (SBIR) grant from the National Institutes of Health (NIH).

Application of the NRF to 3-D structure generation from X-ray crystallography data (ASTER-X) has been successfully prototyped under the auspices of an NIH SBIR grant. Results indicate that the NRF will enable similarly dramatic computational speed improvements over conventional X-ray structure generation methods, as the NRF has achieved for NMR. A provisional patent application has been filed.

"The maturation of the ASTER/NRF technology could not be coming at a better time," noted Carlos E. Padilla, vice president of research and development at SBI-Moldyn, and co-inventor of ASTER with Valeri I. Karlov, SBI-Moldyn's principal scientist. "Fast industrial scale structure generation is where the industry is headed, and with its dramatic computational speed performance, ASTER is well-positioned to play a significant role in the NMR and X-ray part of the movement."

About Structural Bioinformatics Inc.

SBI is a world leader in computational proteomics -- the large-scale generation and use of protein structure and protein structural information. The company has developed advanced technologies to generate highly refined 3-dimensional structural models of proteins from primary genetic information and commercializes these technologies through its structural database products and through drug discovery collaborations with leading pharmaceutical companies. SBI has offices and research facilities in San Diego; Cambridge, Mass. and Horsholm, Denmark. More information about SBI can be found on the company's Web site at: www.strubix.com.