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BIND to open London office, hire more curators

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The Blueprint Initiative announced in early August that in addition to its current offices in Toronto and Singapore, it will be opening a new office in London to collaborate with Nature Publishing Group and further expand the Biomolecular Interaction Network Database, or BIND.

BIND is a database of records documenting molecular interactions, including those between proteins, DNA, RNA, ligands, molecular complexes, and other biological molecules.

“We’re trying to get to the point where capturing [molecular] interactions from journals is not so much like catching rain in a teacup,” says Christopher Hogue, the principal investigator at Blueprint Initiative, a research program based in Toronto’s Mount Sinai Hospital. “It’s hard to do. The first step is to get the tier-one journals involved. Science and Nature have both endorsed our curation process.”

Endorsement of the database by major journals is an important step in producing a comprehensive molecular interaction database because it could lead to a more automatic process where scientists submit information to the database themselves, Hogue says, in a system more like sequence repository GenBank.

By encouraging scientists to submit information to the database themselves, journals could ease the burden on curators to find and enter data using published articles. A submission system would also make the database more up to date, with molecular interactions entered in the database while the paper is still in the pre-publication process.

Blueprint’s Singapore offices opened in February of this year, and London offices were expected to open by January 2005.

— Tien-Shun Lee

Datapoint: BIND Statistics (As of Aug. 27, 2004)
97,378 Interactions
1,985 Complexes
8 Pathways

PATENT WATCH

US Patent No. 6,780,582. Arrays of protein-capture agents and methods of use thereof. Inventors: Peter Wagner, Steffen Nock, Dana Ault-Riche, Christian Itin. Assignee: Zyomyx. Issued: August 24, 2004.

Covers arrays of protein-capture agents useful for the simultaneous detection of many proteins, which are the expression products, or fragments thereof, of a cell or population of cells in an organism. Also covers methods of making and using the arrays of protein-capture agents. The invention arrays are particularly useful for various proteomics applications, including assessing patterns of protein expression and modification in cells.

US Patent No. 6,777,239. Epitope-captured antibody display. Inventors: William Dower, Steven Cwirla. Assignee: XenoPort. Issued: August 17, 2004.

Covers reagents and methods for detecting target proteins in a sample. The reagents include a replicable genetic package, a protein displayed on an exterior surface of the package that is expressed from a heterologous nucleic acid borne by the package, and one or more antibodies complexed with the expressed protein and which have an open binding site for a target protein. The reagents can be utilized individually or as part of a library or an array to bind target proteins within protein samples to form one or more complexes.

NIH issues an RFA entitled “National Technology Centers for Networks and Pathways” to develop novel, broadly applicable proteomics technologies, including instrumentation, biophysical methods, reagents, and infrastructure technologies. The deadline for letters of intent is Jan 18, 2005; applications are due Feb. 22.

GenData Research and Batelle announce that they have entered into a collaboration to identify, develop, and commercialize biomarkers for chronic obstructive pulmonary disease using mass spectrometry and NMR techniques.

The Blueprint Initiative research program announces that it has surpassed its milestone for submissions to BIND, reaching almost 100,000 records a full year ahead of schedule.

NIAID awards Caprion Pharmaceuticals a $13.1 million biodefense contract to employ its quantitative protein profiling technologies to analyze pathogen and host proteins as a means of discovering new immunotherapy targets, vaccines, and diagnostic biomarkers.

Nonlinear Dynamics forms a collaboration with Matrix Science to integrate the companies’ proteomics software products, including Mascot and Nonlinear’s protein informatics system.

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