4SC, the Institute for Systems Biology and Molecular Mining Team partner with IBM to advance drug discovery

Somers, Stuttgart 10 June 2002IBM seems to be cruising the life sciences highway with its powerful solutions for the biotechnology, genomic, e-health, and pharmaceutical markets. The biotechnology company 4SC AG has decided to use IBM Linux Cluster technology for drug discovery. The Institute for Systems Biology (ISB) has selected IBM to provide its infrastructure technology. In addition, IBM and Molecular Mining Corporation (MMC) will collaborate on technology offerings which can help researchers analyse gene and protein expressions, discover relationships among the data to diseases, and predict drug responses.

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The installation of 256 double-processor eServers from the xSeries 330 and one xSeries 342 will begin immediately at 4SC AG, a German drug discovery and development company that derives its competitive advantage from bridging the gap between disease targets and novel drug candidates with its unique cheminformatics-based technology platform. IBM's high-performance computing solution will enable the Munich-based company to produce computer simulations of drug targets and lead substances for the development of new drugs.

Servers will run 4SC's proprietary Virtual High Throughput Screening technology (vHTS), which calculates the biological activities of millions of molecules on the basis of protein structures, homology modelling or the biological activity of existing compounds. This will enable 4SC to offer substantial time and cost savings for the advancements of drug candidates to the development phase. The powerful IBM eServers are equipped with self-diagnosis and self-healing technology from IBM's own eLiza project. Due to this technology, the computers are, to a large extent, capable of self reporting and repairing their own system errors, thereby avoiding downtime.

"By combining chemistry, biology and computer-based screening, we are able to accelerate the development of active substances for new kinds of therapeutic drugs. With our proprietary Virtual High Throughput Screening technology (vHTS), we can calculate the biological activity of millions of molecules in a very short time. In order to calculate the biological activity of molecules even more rapidly within our constantly growing database, we had been looking for a reliable IT infrastructure that would provide the processing requirements. IBM's Life Sciences division was the obvious choice to provide this technology", stated Dr. Ulrich Dauer, CEO of 4SC.

4SC decided on the IBM eServers from the xSeries 330 and 342. In the weeks to come, a total of 257 of these computers with 514 processors will be installed at the 4SC Martinsried laboratories, supplementing the company's current computing capacity. The eServers are equipped with fast Intel Pentium III processors as well as IBM Director software, a control and surveillance programme that detects and repairs possible system errors before they can lead to failures and downtimes.

This technology was developed as part of IBM's eLiza Initiative, a group focused on the design of a cross-platform system to prevent server failure. Similar to the body's immune system, which operates without our awareness, this self-healing technology performs without the intervention of a systems administrator. "This combination of fast processors and eLiza technology makes it easier for our clients to administer their servers", commented Thorsten Bartelt, Head of IBM's Life Sciences Division. "Server failures are avoided. Moreover, the servers of the xSeries Family are an economical IT solution that is reliable, quick to install and easy to operate. For a growing biotechnology company like 4SC, these are irresistible advantages."

4SC's therapeutic focus and research activities centre on infectious and select hyper-proliferative diseases. Three projects, for rheumatoid arthritis, malaria and bacterial infections, are currently in preclinical efficacy and pharmaco-kinetics studies. The vHTS technology has the unique ability to screen 4SC's continuously growing database containing more than two million compounds or its virtual combinatorial libraries containing up to ten million compounds in a 24 hour period.

In turn, the Institute for Systems Biology will use IBM servers, storage and data integration products to support its research on protein-protein interactions to better understand and predict diseases, and identify potential preventions and treatments. Through the agreement, announced at the BIO 2002 Conference, IBM and ISB will also explore research collaborations in systems biology. ISB is specialised in this emerging field, which uses computer technology to model not just the functions of individual genes and proteins, but their complex interactions within a cell, tissue, organ or whole organism.

"This research is the essence of what ISB is all about", explained Co-founder and President Dr. Leroy Hood. "You can't learn about systems by studying one gene or protein at a time. The information from genes and proteins is complex and requires tremendous computational firepower. The technology framework from IBM will give us the power we need to quickly analyse and integrate the data, and accelerate our research efforts."

ISB is replacing products from non-IBM vendors with the IBM systems, including a 64-node IBM eServer xSeries 1300 Cluster, with two micropressors per node. This highly scalable, prepackaged cluster will be used to process data from a network of mass spectrometers, which identify and analyse proteins, critical steps in the process of determining protein-protein interactions. ISB researchers will use IBM's DiscoveryLink software to quickly and seamlessly integrate proteomics data in disparate formats and file types, from a variety of public and private data sources. Deployment of ISB's new information technology infrastructure is expected to be complete in the third quarter of 2002.

The Institute for Systems Biology was founded by Dr. Leroy Hood, Dr. Rüdi Aebersold and Dr. Alan Aderem in 2000 and has grown to a faculty of eight and a staff of more than 170. Dr. Hood, the Institute's president and director, led the development of the automated DNA sequencing technology which enabled the Human Genome Project and was among the small group that advocated for the effort in 1985.

Associate Director Alan Aderem, a prominent immunologist and cell biologist and pioneer in the study of innate immunity, has provided scientists with fundamental insights into the functioning of the macrophage. Dr. Aebersold, an international expert in analytical protein biochemistry and proteomics, leads a research group at the Institute which is focused on developing new methods and technologies for understanding the structure, function, and control of complex biological systems.

Within a third partnership, IBM and Molecular Mining Corporation (MMC) will apply state-of-the-art information technology toward solving one of the most complex problems in life sciences today: understanding how interactions among genes and proteins can trigger biochemical reactions in cells and cause diseases such as cancer, AIDS, and depression. It will also aim to increase scientific understanding of why small genetic variations within individuals can cause significantly different responses to particular therapies.

MMC's product offerings will be augmented by IBM's DiscoveryLink data integration software. These include GeneLinker Gold and GeneLinker Platinum, powerful analysis and visualisation tools for mining gene and protein expression data. DiscoveryLink enables scientists to easily search diverse data sources and file types and quickly get a single-format view of information, without moving the data or changing its underlying format.

In addition to joint sales and marketing efforts, IBM and MMC will explore research collaborations in areas such as visualisation, pattern discovery, and gene expression analysis. Through the agreement, IBM becomes a preferred information technology partner provider for MMC and MMC becomes a preferred advanced Life Sciences data mining partner provider for IBM. GeneLinker Platinum will be shipped on IBM Intellistation professional workstations, and new MMC products will become generally available first on IBM middleware, workstations, and server platforms.

Also, MMC will use IBM technologies for internal development. MMC's IT infrastructure will include a cluster of powerful IBM eServer xSeries systems running Linux and be supported by the IBM Life Sciences Framework, an open, scalable architecture for integrating data, applications, and systems across the entire drug discovery and development cycle. MMC specialises in the prediction of complex biological behaviour using its unique, proprietary core technology.

The company applies this technology to gene expression, single nucleotide polymorphisms (SNPs) and proteomics data to improve diagnostic and drug target identification and prioritisation, predictive toxicology and drug screening. MMC markets its solutions through shrinkwrap software sales, strategic co-development of software, and collaborative relationships.


Leslie Versweyveld

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