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Genvea Biosciences, Insightful, Accelrys, Definiens, University of Washington


Genvea to Provide Software for Singapore Bioinformatics Center

Informatics consulting firm Genvea Biosciences of Singapore said last week that it has entered a bioinformatics software infrastructure partnership with the Bioinformatics Research Center (BIRC) at Nanyang Technical University and Hewlett-Packard.

Hewlett-Packard (Compaq, at the time) entered into a partnership with the BIRC in March 2002, when it agreed to provide an AlphaServer supercomputer for the center [BioInform 03-25-02].

Genvea said it would provide a programmable software infrastructure for the BIRC “suitable for the rapid-prototyping, development, and deployment of new applications in bioinformatics and data-driven life sciences research.”

Financial terms of the agreement were not provided.

Genvea also plans to conduct workshops, seminars, and lectures at the BIRC, and will sponsor an annual prize for the best graduate or undergraduate project at BIRC based on its system.

Insightful Licenses Affy APIs

Insightful last week said that it has licensed the Affymetrix application programming interfaces for use in its S+ArrayAnalyzer software for the statistical analysis of microarray data.

The incorporation of the Affy APIs makes S+ArrayAnalyzer fully compatible with all Affymetrix microarray systems, Insightful said, including the new GeneChip Operating Software (GCOS) output and the entire installed base of Affymetrix instruments and scanners.

Incorporation of the APIs in S+ArrayAnalyzer will be available by the end of 2003, Insightful said.

Strand Genomics, Iobion, and Rosetta Biosoftware have also announced similar licensing agreements for the Affymetrix APIs.

Financial Express: Accelrys to Employ 102 at Bangalore R&D Center

India’s Financial Express news service last week reported that Pharmacopeia’s software subsidiary Accelrys plans to hire up to 102 employees for its recently opened R&D center in Bangalore.

The center, called Accelrys Software Solutions, currently employs 50 people, but plans to hire at least 50 more in the next six months, the paper reported.

Pharmacopeia CEO Joseph Mollica said the company expects the Bangalore facility to “lead the way in areas like quality control and quality assurance in terms of the informatics products of the company,” according to the Financial Express.

Definiens Signs Distribution Agreement with Serva Electrophoresis

Munich-based software firm Definiens said last week that Serva Electrophoresis of Heidelberg will sell its Proteomweaver 2D gel analysis software as part of its product portfolio.

Serva sells a range of biomedical products related to electrophoresis, including albumins, antibiotics, buffers, dyes, enzymes and enzyme inhibitors, media, proteins, salts, and surfactants.

Serva will package Proteomweaver with its other products, Definiens said.

Baker Team Synthesizes Novel Protein Based on In Silico Design

A team led by David Baker at the University of Washington has successfully constructed a novel protein using a computational protein design methodology.

The researchers describe their work in the Nov. 21 issue of Science.

According to the researchers, the approach is a valuable method for understanding the mechanisms of protein folding, and is also a first step toward engineering artificial protein enzymes for use as medicines or industrial catalysts.

Baker’s team used an iterative computational strategy that drew from both sequence design and structure prediction to design a globular 93-residue alpha/beta protein called Top7 that is not present in the PDB. The approach integrated protein design algorithms that identified low-energy amino acid sequences for a fixed protein structure with protein structure-prediction algorithms that identified low-energy protein structures for a fixed amino acid sequence.

“If you draw on the back of an envelope some arbitrary protein structure, it might be that there is simply no amino acid sequence that will fold up to that structure,” Baker said in a statement. “We had to develop methods to computationally sample possible structures similar to the one drawn on the back of the envelope, searching for a conformation for which there exists a very low-energy amino acid sequence.”

Baker and his colleagues used methods developed for the Rosetta ab initio protein structure prediction methodology to guide the process. They first specified a starting backbone conformation and then used RosettaDesign (available at to identify the lowest-energy amino acid sequence for the conformation. The team then kept the amino acid sequence fixed and used the Rosetta structure prediction methodology to identify the lowest-energy backbone conformation for the sequence. After repeating the sequence optimization and structure prediction steps 10 times, they arrived at a protein sequence and structure predicted to have lower energy than naturally occurring proteins in the same size range.

In order to validate its in silico design, the team synthesized Top7 and determined its three-dimensional structure using x-ray crystallography. “One of the real surprises came when we actually solved the crystal structure and found it to be marvelously close to what we had been trying to make,” said Baker.

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