Pharmaceuticals & Bioinformatics

Drug discovery, lead candidate selection and pre-clinical development are undergoing rapid changes, driven in part by scientific advances in areas such as combinatorial chemistry, discrete optimization and high throughput compute technology.

The pressure to accelerate drug discovery and development is increasing, especially in the phases leading toward early clinical testing where a clear bottleneck exists. Fierce competition, market positioning and the need for targeted ROI demand that companies continue to research and develop critical technologies to gain competitive advantage.

Optimization Opportunity

The European clinical trials market is expected to reach €30B by 2012. On average it takes circa 10–15 years and €600M to develop a major new medicine, about 40% of which is spent on pre-trial development.

The growth in the value of the drug development market can be attributed to the increasing number of drugs that need to be tested. For example, less than 1 in 10,000 compounds which are initially tested make it through the clinical trials process. An average of 250 enter pre-clinical testing, 10 make it through to clinical trials, and only one is approved by the regulator to market.

Exploiting better computational methods during the R&D phase can decrease the probability of a drug failing during clinical trials, improve the estimate of the percentage of patients for which a drug will be effective or can reduce the potential of off target effects like toxicity are critical to reducing the time is takes to reach the market. Bringing a new drug to market one year early can save more than €100M, excluding the upside of market share and brand positioning.

Satalia provides products and services for solving hard optimization problems. The Satalia technology is based on world-leading research and improves performance by several orders of magnitude over current industry standards. Satalia’s new technology model and performance on standard public benchmarks is illustrated below.`

Sample Applications

Hard optimization problems exist in a wide variety of areas in the pharmaceutical and biotechnology industry. Here are just some of the problems Satalia can solve:

• Haplotype Inference - Solving even the hardest of Haplotype Inference by Pure Parsimony problems

• Gene Regulatory Networks:Genomic Distance Calculation - New approaches to deciphering the dynamics of gene regulatory networks & computing the exact genomic distance between two genomes in the presence of duplications

• Protein Structure Prediction - Techniques to predicting the 3D structure of a protein from its amino acid sequence

• Pedigree Checking - Accelerating verification of the correctness of genetic relationships of individuals

Other core computational problems in bioinformatics include:

• Multiple Alignment - sequence alignment of three or more biological sequences, generally protein, DNA, or RNA

• Shortest Common Superstring - find a shortest possible common supersequence of two sequences

• Double Digest - constructing physical maps of DNA sequences

• Protein Threading - aligning each amino acid in the target sequence to a position in the template structure, and evaluating how well the target fits the template

• Bi-Clustering - simultaneous clustering of the rows and columns of a matrix.

• Pseudoknot Prediction - finding optimal secondary structures of RNA sequences

You benefit by saving millions of dollars through optimizing your processes and delivering more reliable products. Stop spending more and more on expensive resources - staff and infrastructure - to solve these problems, let Satalia solve them for you.