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Distributed Protein-Folding Project, Inpharmatica, Tripos, Locus Pharmaceuticals, Definiens, Proteomics Informatics, Ben Franklin Award


ISB, IBM, UD, U Wash Embark on Distributed Protein-Folding Project

The Institute for Systems Biology, IBM, United Devices, and the University of Washington last week launched the Human Proteome Folding Project — a distributed computing project that will be the first to run on the World Community Grid, an effort started by IBM and others to leverage unused computing time of participants for a variety of projects.

Like other distributed protein-folding projects — such as [email protected] ( and the Distributed Folding project at the Samuel Lunenfeld Research Institute ( — the Human Proteome project will split the problem of folding a single protein into millions of smaller “work units” that will run on the desktops of volunteers who sign up at

In addition to volunteer PCs, the World Community Grid is powered by IBM eServer p630 and x345 systems and IBM’s Shark Enterprise Storage Server running the DB2 database software.

Future projects will be selected by a newly created World Community Grid Advisory Board that will evaluate proposals from research organizations “seeking to conduct humanitarian research using grid computing technology,” IBM said.

The advisory board, which includes members from the National Institutes of Health, the Doris Duke Charitable Foundation, the Markle Foundation, the Mayo Clinic, Oxford University, and the World Health Organization, is expected to oversee five to six projects a year.

Inpharmatica to Receive $1.5M, Future Royalties in Expanded Serono Deal

Inpharmatica said last week that it has expanded a drug-discovery collaboration with Serono that began in 2001.

Under the terms of the expanded agreement, Serono will pay Inpharmatica $1.5 million for “additional rights” to proteins identified using Inpharmatica’s PharmaCarta informatics platform.

Inpharmatica said that the collaboration has identified more than 200 novel protein sequences so far, and that the expanded agreement “will encompass a significant commitment from both companies toward their characterization and exploitation.”

The expanded deal includes the additional use of Inpharmatica’s wet lab resources to support the validation of the proteins.

In addition to the up-front payment, Inpharmatica is also entitled to milestones and royalties from any resulting products.

The news comes a week after Inpharmatica secured $26 million in a VC funding round [BioInform 11-15-04].

Pfizer Renews Global License to Tripos Software

Tripos said last week that it has extended a global software license agreement with Pfizer in “a multimillion-dollar, multiyear” deal.

The companies first entered into a wide-area network partnership in January 2001.

Tripos said that Pfizer is using a “broad array” of its drug-discovery software, including its Sybyl and Unity programs.

Locus Pens Deal with Dow AgroSciences

Locus Pharmaceuticals said last week that it will use its fragment-based computational drug-design technology in a “multi-stage” research collaboration with Dow AgroSciences, a subsidiary of the Dow Chemical Company.

Locus said it will use its technology to discover and develop small-molecule compounds to treat fungal targets identified by Dow AgroSciences.

Locus said it will receive “certain milestones and royalties” from the deal, and will have an exclusive option to human therapeutic applications. Additional financial terms were not provided.

Definiens Partners with Beecher on Tissue Microarray Software

Definiens said last week that it will partner with tissue microarray instrumentation provider Beecher Instruments to develop software for tissue microarray image analysis.

Under the terms of the agreement, Beecher is using Definiens’ Cognition Network Technology to develop applications for automated tissue microarray analysis.

Current image analysis software requires extensive user interaction to properly identify cell populations, select regions of interest for scoring, optimize analysis parameters, and organize the resulting raw data, Definiens said. The suite of tools that Beecher has developed with Definiens’ technology, called TMAx, can automate this process, according to the companies.

ISB Offers Course on Proteomics Informatics

Seattle’s Institute for Systems Biology said last week that its NHLBI Proteome Center will be offering a course on proteomics informatics Jan. 31-Feb. 4.

The course is designed to instruct proteomics researchers in the use of a suite of software tools designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using the ICAT reagent labeling method, multi-dimensional chromatography, and tandem mass spectrometry.

Further information and application materials are available at

Bioinformatics.Org Seeks Nominations for Ben Franklin Award

Nonprofit bioinformatics open source advocacy Bioinformatics.Org is seeking nominations for its Benjamin Franklin Award in Bioinformatics, which is presented annually “to an individual who has, in his or her practice, promoted free and open access to the methods and materials used in the scientific field of bioinformatics.”

Past recipients include Lincoln Stein, Jim Kent, and Michael Eisen.

The nomination deadline is Dec. 1. Further information and nomination forms are available at

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