White Papers

Environmental Chemistry and Toxicology

Abstract: This paper describes the use of a centralized data management system that allows manufacturing organizations to effectively manage regulatory compliance. The Accelrys Environmental Chemistry and Toxicology (ECT) Solution is a customizable “scientifically-aware” platform to streamline monitoring, analysis, and reporting of chemical by-products for the purposes of regulatory compliance. This scientifically-aware solution inherently allows for QSAR analysis, chemical similarity searching and other read-across techniques to maximize the value of all data. The scientific platform can easily be configured to automatically predict biodegradation products, physical properties, ADME and Toxicology properties and many other descriptors. The solution can also be configured to automatically compare any of these properties to codified business rules specific for each facility. These, and many other capabilities can automatically be presented on interactive dashboards or on REACH, MSDS or other formal documentation.
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Scientific Business Intelligence™ Solutions

One of the major challenges facing the scientific and clinical research communities is the inability to access, aggregate and mine scientific data across an enterprise organization. Data remains locked in silos, causing productivity and decision making to suffer, and ultimately impeding an organization's research efficiency. By successfully harnessing disparate data sources and software applications, organizations position themselves to apply their data in an intelligent, focused manner, thereby improving productivity, decision making and research efficiency. However, such efficiencies have eluded many scientific and clinical research organizations because traditional business intelligence (BI) technologies cannot handle advanced scientific data processing and analysis. This lack of a readily available BI solution has forced organizations to make do with vendor-specific solutions, drain in-house development resources by building customized solutions, or struggle with sharing data among incompatible point products. Accelrys' proven history of delivering innovative modeling, simulation and informatics software for life and materials sciences, as well as its open and standards-based scientific operating platform, positions it to deliver scientifically-relevant BI solutions that meet the needs of the scientific and clinical research communities.
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Measuring the Return on Modeling and Simulation Tools in Pharmaceutical Development

Based on in-depth interviews with research scientists in pharmaceutical development, market research firm IDC concludes that there is a significant return on investment (ROI) to be realized from the use of modeling and simulation software tools. The research was based on conversations with researchers at major
pharmaceutical companies and academia and suggests a cumulative ROI of the order of $3–10 for every $1 invested in these tools.
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Modeling and Simulation: The Return on Investment in Materials Science – an IDC Chemicals Industry White Paper

Market research firm IDC’s recent study concluded that for each dollar invested in modeling and simulation software and its support infrastructure, $3 to $9 was returned to the company in incremental revenue and costs savings. The source of the return on investment included:
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Toward Nanomaterials by Design: A Rational Approach for Reaping Benefits in the Short and Long Term

Scott Mize, President of the Foresight Institute (www.foresight.org), describes a rational approach to Nanomaterials by Design and explains why nanotechnology companies must adopt it to most effectively and efficiently discover, develop, and manufacture new products. At the core of Rational Nanomaterials Design are modeling, simulation, and informatics software tools, which have been demonstrated to reduce development costs, speed time to market, and enable designers to develop better materials with a greater focus on end-user application requirements.
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High Performance Computing with IBM

With the average cost of a new small molecule drug hovering at $800 million today vs. $200 million in 1987 [1], pharmaceutical and biotech companies are in urgent need of innovations to improve profitability. The problem may be attributed to the deteriorating rate of compounds in Phase I of clinical development reaching the market, which CMR International estimated to be at 23% in 1994-1996, 15% in 1995-1997, and 11% in 1996-1998 [2]. To improve this rate, pharmaceutical and biotech companies turn to informatics (bioinformatics and cheminformatics included), that help scientists run more virtual experiments, modeling and simulation than ever before. This, in turn, drives a need for scalable and efficient data management and analysis solutions.

This white paper discusses an implementation of a data pipelining analysis platform that caters to a large number of users in an environment with multiple, heterogeneous databases as described above. The work is a collaboration between SciTegic and IBM, and includes benchmarking results of this solution and its configuration. PDF format.
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Compound Acquisition using Pipeline Pilot

With the advent of high-throughput screening, life science companies have the capacity to routinely screen hundreds of thousands to millions of compounds in the laboratory in a very short time. An immediate problem is to ensure that a large, high quality collection of compounds is available to match the screening capacity. However, many smaller and newer companies do not posses a significant in-house compound collection. Even at the largest pharmaceutical companies, historical compound collections typically do not contain a sufficient number of compounds to keep the screens busy. In addition, these historical collections may suffer from issues of compound quality and diversity. Two approaches have been taken to fill the screening pipeline - the acquisition of compounds from external collections, and the use of high throughput combinatorial chemistry to produce large numbers of compounds. This application note focuses on using Pipeline Pilot in the compound acquisition process, PDF format.
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Enumerating Combinatorial Libraries using Pipeline Pilot

Combinatorial chemistry techniques are a routine part of lead generation and lead optimization. With the capability to synthesize large numbers of compounds and the use of automated synthesis, computational methods are an integral part of the combinatorial chemistry process. A number of computational tasks are important in the preparation of combinatorial libraries, including:

• Identification and selection of reagents.
• Computational definition of virtual libraries for design, or real libraries for synthesis, and the enumeration of the compounds within those libraries.
• Subset selection from a virtual library: diverse selections for lead generation or focused selection for lead optimization.
• This application note focuses on the first two tasks, PDF format.

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