Vertex Pharmaceuticals installs supercomputer to accelerate drug discoveryCambridge 13 August 2001 Vertex Pharmaceuticals installed a new supercomputer cluster, one of the most powerful in the world dedicated to in silico drug design applications, the company claims. This cluster will perform parallel computations using proprietary software and broad in-house modeling expertise that supports Vertex's structural biology, combinatorial chemistry, medicinal chemistry, high throughput screening, bioinformatics, and pharmacology groups. The new supercomputer cluster was created for Vertex by Blackstone Computing. The initial installation will consist of 56 computers and 112 computing processors (933 MHz Pentium III) providing approximately 110 Gflop/s at theoretical peak computing power, which is approximately five times faster than Vertex's current supercomputer cluster. The system is designed to be scalable, and will allow further expansion to 450 computers and 900 processors to keep pace with Vertex's computing needs.
The supercomputer will also provide a powerful tool for
analyzing complex data and information generated using industry-leading cell-
based assays and ultra-high throughput screening approaches. The new cluster
represents a key component of the technology infrastructure that is expected
to accelerate productivity in Vertex's gene family-based research.
A distinguishing
feature of the new cluster is a high-speed, low-latency interconnect, which
guarantees rapid information exchange between processors and enhances the
solution of complex numerical simulations.
Parallel computation is playing an increasingly important role in
integrated drug discovery by allowing dramatically accelerated screening of
large computer-generated chemical libraries, enhanced capabilities in the
measurement of protein-inhibitor interactions in silico and increased power to
analyze complex data sets from high throughput screening. The identification
and selection of potent lead drug candidates through analysis of molecular
dynamics can also be facilitated through parallel computation.
Vertex has developed a substantial library of proprietary software and
algorithms that can harness the power of parallel computation for the purposes
of small molecule drug design, including: in silico screening techniques that
predict pharmacological properties of candidate drugs such as bioavailability,
toxicity, half-life, and blood-brain barrier penetration; molecular modeling
and ligand docking algorithms that help to identify promising chemical classes
of inhibitors; and quantitative structure activity relationship (QSAR)
approaches that help to optimize leads based on novel functions that are fit
to experimental data. Vertex's software development efforts are now being
expanded in the area of gene families, with novel applications that enable
analysis of a chemical library for selectivity among clusters of similar
protein targets, and comparison of multiple libraries based on a single
protein target.
Vertex is pioneering the field of chemogenomics, which represents the
intersection of medicinal chemistry and the human genome-the universe of all
the possible drugs that can be directed at all of the possible drug targets.
With the insight that genes and the proteins they encode can be grouped as
families according to structural similarity, Vertex is designing drugs in
parallel for multiple targets in gene families. In July 2001, Vertex acquired
Aurora Biosciences, providing Vertex with industry-leading assay development,
screening and cell biology technologies that are expected to enhance Vertex's
capabilities in new gene families.
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