Schrödinger Developing Combinatorial Glide, Expects Release by Year End
Schrödinger is developing a version of its Glide docking software with “combinatorial” ligand-design capabilities that could be on the market by the end of the year, according to company officials.
Richard Friesner, a chemistry professor at Columbia University and founder of Schrödinger, described the algorithm, called CombiGlide, at CHI’s Virtual Screening and Structure-Based Drug Design Conference in Boston last week. The approach docks a “core” ligand fragment, and then adds “libraries of side chains” to the core fragment in order to arrive at a molecule with optimal binding capabilities.
Shi-Yi Liu, vice president of marketing at Schrödinger, told BioInform that the company is currently working on a commercial version of the software, and that it could be launched by the end of the year.
Liu stressed that the launch date is tentative.
NIST Adds 2D Inhibitor Data, Chem-BLAST to HIV Protein Structure Database
The National Institute of Standards and Technology has released a beta version of a new database containing 2D structural information for HIV protease inhibitors.
Speaking at CHI’s Virtual Screening and Structure-Based Drug Design conference, Thalapady Bhat, senior scientist in NIST’s biotechnology division, said that a beta version of the 2D chemical structure resource went live last week.
The database is a component of the HIV Structural Reference Database (HIVSDB) that NIST launched in July, which contains HIV-related protein structures derived from the Protein Data Bank as well as previously unpublished structures from other resources. According to Bhat, the database contains 70 percent more HIV protease structures than are available in the PDB.
The new resource adds 2D chemical structures for around 500 active HIV protease inhibitors, Bhat said.
HIVSDB, available at http://xpdb.nist.gov/hivsdb/hivsdb.html, is a collaboration between NIST, the National Cancer Institute, and the National Institute of Allergy and Infectious Diseases. Bhat said that the database has recorded nearly 2 million hits so far.
Bhat said that the new 2D chemical information is fully integrated with the 3D protein structural data, and that NIST has indexed the 2D information so that users can search the database with text strings or chemical features using a new algorithm called Chem-BLAST (Chemical Block Layered Alignment of Structure Technique).
Blueprint, Germany’s IBI to Coordinate Curation of BIND, MIPS
Canada’s Blueprint Initiative and Germany’s Institute for Bioinformatics last week announced that they had signed a memorandum of understanding to coordinate activities between Blueprint’s BIND (Biomolecular Interaction Network Database) and IBI’s MIPS (Munich Information Center of Protein Sequences).
Under the terms of the agreement, the IBI will “adopt Blueprint data assembly practices” and will become an “active participant in the curation of peer-reviewed scientific data” into BIND.
Blueprint will train MIPS curators to keep up with an estimated 2,000 physical interactions published in the scientific literature per month.
IBI and Blueprint said they also plan to coordinate efforts to secure funding in support of specific journal curation backfilling efforts.
Peakdale to Use BioLeap’s Computational Drug-Design Skills in New Collaboration
Peakdale Molecular said last week that it is partnering with computational drug-design firm BioLeap in a project to design and synthesize kinase libraries, with the initial project targeting the c-Abl tyrosine kinase.
Peakdale, a chemical synthesis firm, will have access to BioLeap’s proprietary technology for calculating the free energies of interaction between small-molecule fragments and biomolecular structures.
According to BioLeap, the approach is able to predict sites with tightly bound waters that cannot be seen in crystallography.
EUropean PAtent Office Licenses Xennex’s GeneCards for Prior-ARt Searching
Xennex said last week that the European Patent Office has licensed its GeneCards database “to assist in the review and approval of patent applications in the life sciences area.”
Financial details of the agreement were not disclosed.
GeneCards will be used at EPO sites in Munich and Berlin, Germany; The Hague, the Netherlands; and Vienna, Austria. EPO Members States’ national offices will also have access to the database to conduct prior-art research and to retrieve relevant information to support their patent-related activities.
Xennex said that several IP law firms are also using the database for prior-art searching, including Lahive & Cockfield, a Boston-based IP law firm that specializes in biotechnology patents.
Ardais Sells Biorepository Business to Cytomyx, Will Focus on Informatics
Ardais last week sold its biorepository business to Cytomyx Holdings for $3.0 million in a move to focus its activities on its biospecimen-management software business.
The sale of the biorepository “completes its strategic evolution to a translational medicine solutions provider,” Ardais said in a statement.
Last year, the biorepository business unit had $3.7 million in revenues. Ardais did not disclose annual revenues for its software business.
As part of the transaction, Cytomyx has entered into a strategic collaboration under which it will gain access to the Ardais System, a suite of software applications, operating procedures, proprietary supplies, and data standards that integrate biorepository operations at multiple geographic sites.
Genstruct Extends its PathArt License
Jubilant Biosys said last week that Genstruct has extended its license to Jubilant’s PathArt database.
Genstruct has been using the database for more than a year.
Financial terms of the agreement were not disclosed.
Advanced Biological Laboratories Licenses Stanford HIVdb Algorithm
Advance Biological Laboratories said last week that it has signed a license agreement to use Stanford University’s HIVdb resistance interpretation algorithm in its ViroScore HIV report, which enables physicians to select the best therapy for an HIV patient based on past and current resistance to HIV drugs.
ABL sells the resistance interpretation platform to diagnostic companies, HIV researchers, and individual physicians treating HIV.
The ViroScore suite of tools includes a database for storing genetic sequence data, analysis tools for reporting on the relationships between clinical outcomes and virus mutations, phylogenetic analysis of sequence groups, and numerous tools to assist physicians and researchers with complex genetic data.
Elsevier Plans to Deliver Electronic Lab Notebook in 2006
Elsevier MDL said last week that it has launched “a dedicated, phased program” to build an enterprise-strength electronic laboratory notebook for the life sciences, built on its Isentris technology.
The company said the system would be ready for delivery in 2006.
Elsevier said it is “interested in working with customers to identify specific requirements for the new-generation [electronic laboratory notebook]. Research organizations with an interest in defining and validating these requirements should contact an Elsevier MDL account manager.”