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For Immediate Release
Santa Fe, NM,October 12, 2004 - The National Institutes of Health (NIH) has decided to use OpenEye Scientific Software's cheminformatics toolkits to provide key infrastructure for PubChem, a database of small organic molecules containing chemical structure and biological activities information. PubChem is being developed by the National Center for Biotechnology Information (NCBI) as part of the Molecular Libraries and Imaging component of the NIH Roadmap Initiative. "I am excited to see our software built into PubChem," says Roger Sayle OpenEye's Vice President of Bioinformatics. "It's gratifying that our software will be part of such a useful public resource."
PubChem will offer researchers public access to an array of structure and activity information for a diverse set of small molecules. It is organized as three linked databases, Substance, Compound, and BioAssay, within the Entrez/PubMed information retrieval system. PubChem contains the results of high-throughput biological screening experiments, and, when possible, PubChem's records are linked to other NCBI databases, such as the PubMed scientific literature database and NCBI's 3D protein structure database.
"Validation and standardization of chemical structure data is critical to PubChem, since it allows us to compute properties, descriptors, and similarity relationships among entries in an accurate and uniform manner." says Steve Bryant, Senior Investigator in charge of PubChem at the NCBI. "We have used OpenEye's software for important steps in our processing pipeline and have found it to be extremely useful. It has allowed us to get PubChem up and running far more quickly than would have otherwise been possible."
Within PubChem, OpenEye's OEChem toolkit is used for file I/O and molecular data handling, substructure pattern matching, stereochemistry and aromaticity perception, and valence bond canonicalization, among other things. OpenEye's OGHAM is being used to assign correct IUPAC names to chemical structures and will also be used to generate structures for the cases where the dataset has only names. Future plans for PubChem include property predictions using additional software from OpenEye.
Along with the recent decision by the Research Collaboratory for Structural Bioinformatics (RCSB) to use OpenEye's cheminformatics toolkits to curate and depict the Protein Data Bank (PDB) ligand dictionary, the NIH's decision is a clear indication of the speed and robustness of OpenEye's technology for large and diverse sets of chemical structures and data. "It has been beneficial working with the NCBI for their project," says Sayle. "Their data includes enough unusual chemistry to make it a nice validation of the software beyond our regular test sets."
About OpenEye
OpenEye Scientific Software was founded in 1997 to develop large-scale modeling applications and toolkits. Primarily geared towards drug discovery and design, areas of application include structure generation, docking, shape comparison, charge and electrostatics, chemical informatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors with PVM, supports 64-bit processing, and runs on Linux, Windows and Mac, as well as HP/Compaq, IBM, SGI and SUN flavors of UNIX.
About the NCBI
Established in 1988 as a national resource for molecular biology information, the National Center for Biotechnology Information (NCBI) creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. For further information on the NCBI, please visit www.ncbi.nlm.nih.gov. For more information about PubChem visit pubchem.ncbi.nlm.nih.gov. More information about the National Institutes of Heath Roadmap Initiative is available at nihroadmap.nih.gov.
About the NIH
Begun as a one-room Laboratory of Hygiene in 1887, the National Institutes of Health (NIH) today is one of the world's foremost medical research centers. An agency of the Department of Health and Human Services, the NIH is the Federal focal point for health research. The NIH's mission is science in pursuit of fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability. The NIH provides leadership and direction to programs designed to improve the health of the Nation by conducting and supporting research: in the causes, diagnosis, prevention, and cure of human diseases; in the processes of human growth and development; in the biological effects of environmental contaminants; in the understanding of mental, addictive and physical disorders; in directing programs for the collection, dissemination, and exchange of information in medicine and health, including the development and support of medical libraries and the training of medical librarians and other health information specialists.
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