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

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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 (http://www.arb-home.de/) and GreenGenes (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi), 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

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.