Skip to main content
Premium Trial:

Request an Annual Quote

Accelrys, SGI Altix, Inpharmatica, Geospiza, Locus Pharmaceuticals, Integrated Genomics, HUPO Brain Proteome Project


It’s Official: Pharmacopeia is Now Accelrys, Emkjer is CEO

Pharmacopeia said last week that its stockholders approved changing the company’s name to Accelrys — the final step in the spin-off of the company’s PDD drug discovery business in order to focus on software sales.

Stockholders approved the name change on May 11, the company said.

Accelrys said it is now “solely focused on delivering scientific software solutions to the life sciences and materials research industries.”

In connection with the spin-off, the Accelrys board of directors appointed Mark Emkjer to serve as president and CEO of the company. Emkjer has been president of Accelrys since December 2002, when he joined from Sunquest Information Systems, where he was president and COO.

Emkjer was also elected to the company’s board of directors. Other members of the Accelrys board of directors include Kenneth Coleman, chairman and CEO of ITM Software; Gary Costley, chairman and CEO of International Multifoods; and Ricardo Levy, chairman of the board of Catalytica Energy Systems.

Pharmacopeia CEO Joseph Mollica resigned from his officer and board positions with Accelrys. In addition, Frank Baldino, James Marino, and Paul Bartlett each resigned from their respective Accelrys board positions.

All four will serve on the board of PDD.

MSKCC to Use SGI Altix System for Pathway Modeling

Memorial Sloan-Kettering Cancer Center’s Computational Biology Center has installed an Altix 3000 supercomputer from SGI as part of its work in cancer pathway simulation and modeling, MSCKK said last week.

The MSKCC center said it will use the 12-processor Altix system running 64-bit Linux with 48 GB of system memory to support its research analyzing gene expression profiles in order to simulate cellular control networks.

Financial terms of the agreement were not provided.

Inpharmatica to Use PharmaCarta Platform in P&GP Discovery Deal

Inpharmatica said last week that it had signed a discovery collaboration agreement with Procter and Gamble Pharmaceuticals based on its PharmaCarta informatics platform.

Under the terms of the agreement, P&GP will fund a project at Inpharmatica to develop computational structural models and identify chemotypes for families of human G-protein coupled receptors. P&GP will also pay additional license fees to use discoveries arising from the collaboration.

Inpharmatica said it would use the Chematica 3D homology modeling component of the PharmaCarta platform in the project, along with its Starlite database to identify tractable chemical hits and GPCR family chemotypes.

Geospiza Licenses WebDrive File Transfer Client in OEM Deal

South River Technologies said last week that Geospiza had agreed to license its WebDrive file transfer client in an OEM partnership.

Geospiza will use WebDrive to transfer data from DNA sequencers to its Finch-Server database management system. WebDrive will also transfer chromatogram files from the Finch-Server to end-user computers.

The WebDrive client “reduces the variability and eliminates the many problems we have with different versions of Windows, browsers, and networking,” said Todd Smith, CEO of Geospiza, in a statement.

Locus Pharmaceuticals Licenses Sarnoff Patent

Locus Pharmaceuticals said last week that it has licensed a “broad” computational drug design patent from the Sarnoff Corporation.

The patent, US No. 6,735,530, entitled, “Computational Protein Probing to Identify Binding Sites,” was issued on May 11 [BioInform 05-17-04].

The patent protects algorithms that use statistical thermodynamic sampling to determine suitable binding sites on a protein target by rapidly calculating how and where selected drug-like molecular fragments adhere to the protein’s surface.

“This core patent is the initial product of a substantial and broad-based patent portfolio covering computational methods for designing drug molecule candidates, as well as the pharmaceutical compounds that evolve from those de novo efforts,” said Yuriy Stercho, director of legal affairs and secretary at Locus.

Locus was launched in 1999 to apply technology developed at Sarnoff to drug discovery. Locus said it is the exclusive licensee of the patented technology and will deploy it in its own drug discovery efforts in the areas of cancer, AIDS, and inflammation.

Integrated Genomics Raises More than $1M in VC Round

Integrated Genomics said it raised more than $1 million in a venture capital financing round last week.

The company did not disclose the exact amount of the funding or the investor.

Integrated Genomics said it plans to use the funds to expand its business, with a “particular focus” in the area of metabolic engineering.

The company also said it plans to develop microarrays for quality control and process optimization based on information in its ERGO bioinformatics platform.

Integrated Genomics specializes in industrial applications for microorganisms.

HUPO Brain Proteome Project to Standardize on Bruker’s ProteinScape

The Human Proteome Organization said last week that its Human Brain Proteome Project has selected Bruker Daltonics’ ProteinScape platform as its standard proteomics workflow and database software suite.

The project is currently in a pilot phase with 18 participating groups in 11 countries in Asia, Europe, and North America.

In a statement, Rolf Apweiler of the European Bioinformatics Institute said, “While we are still working on community standards for proteomics in the HUPO Proteomics Standards Initiative (HUPO PSI), we have here already a software solution with ProteinScape that will be compatible with HUPO PSI and is already usable at this early time point of the HBPP project. This enables all projects participants to communicate with one standard right from the beginning.”

ProteinScape was co-developed by Bruker Daltonics and Protagen of Dortmund, Germany, and is distributed exclusively by Bruker Daltonics.

Workshop Scheduled for Computational Methods in Protein Crystallography

The Cornell High-Energy Synchrotron Source’s Macromolecular Diffraction Facility will host a one-day workshop on computational methods in protein crystallography on June 15.

The workshop will be held in conjunction with the annual user meeting for the Cornell High-Energy Synchrotron Source June 15-16. Scheduled topics include phasing algorithms, data processing, and automatic structure solution.

Further information and registration details are available at


Filed under

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.