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Molecular Modeling Center, Nonlinear Dynamics, CLC Bio, Ariadne Genomics

NIH Awards Burnham Institute $2.1M to Create Molecular ModelingCenter
The Burnham Institute for Medical Research said this week that it has been awarded a three-year, $2.1 million grant from the National Institutes of Health to create the Joint Center for Molecular Modeling in collaboration with the University of California San Diego.
The goal of the center will be to improve computational methods for predicting three-dimensional protein structures from DNA sequences.
Co-principal investigators for the center include Adam Godzik, director of the Bioinformatics and Systems Biology Program at the Burnham Institute; Pavel Pevzner, professor of computer science in the Department of Computer Science and Engineering at UCSD's Jacobs School of Engineering; and Yuzhen Ye and Piotr Cieplak, research assistant professor and staff scientist, respectively, at the Burnham.
It currently takes several weeks or months to solve a protein structure experimentally. While computational methods promise to reduce this time to a matter of minutes, “the quality of such models is generally so poor that they are not useful in many applications, such as drug design,” Godzik said in a statement.
“We have developed tools that allow us to learn from structures already solved and apply that knowledge to improve predicted structures of new proteins,” he said.

Nonlinear Says SameSpots is ‘Fastest Selling’ 2D Software
Nonlinear Dynamics said this week that its recently launched SameSpots image analysis software is its “fastest ever selling 2D analysis software.”
SameSpots was released in March, and the privately held company said that sales so far have exceeded those of the first 18 months after the initial launch of Progenesis, the company’s previous 2D analysis software.
Nonlinear said that SameSpots eliminates post-analysis editing for most experiments, whch “drastically speeds up the 2D analysis process.”

NASA’s Exobiology Program Uses CLC Bio’s Sequencing Software
The Exobiology Branch of the NASA Ames Research Center in Moffett Field, Calif., is using CLC Bio’s CLC combined Workbench bioinformatics software for sequence analysis, the company said this week.
The NASA research group is using the software to analyze sequence data from hypersaline microbial mat systems in parts of Mexico and Egypt.
These microbial mat communities represent some of the earliest known microbial communities on Earth and are thought to have played a significant role in the development of modern oceanic and atmospheric conditions.
Stefan Green, a scientist working at the NASA Exobiology Branch, told BioInform that the group uses a number of publicly available software tools for ribosomal RNA analysis, such as ARB ( and GreenGenes (, and is using the CLC Bio tools primarily for sequence assembly.
Financial terms of the agreement were not provided.

Murex To Use Ariadne’s Pathway Studio for Cancer Therapeutics Development
Ariadne Genomics said this week that Murex Pharmaceuticals has licensed its Pathway Studio software in order to develop computer-based models to identify and validate cancer targets.
Murex is developing cancer therapies based on gene expression data from individual patients.

Financial terms of the agreement were not disclosed.

Filed under

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.