Predictive P450 Toxicology: Metabolism and Polymorphisms. Start date: Feb. 2004. Expires: Jan 2006. Amount: $231,191. Principal investigator: Danni Harris. Institution: Moltech. NIH institute: NIDOCD.
Phase I SBIR supports development of methods for predicting the principal products of CYP450 metabolism of drugs by a combination of ligand-P450 configurational sampling, based on rapid flexible docking, and electronic determinants of metabolism by the active heme species of P450s. The project will be extended to test predictions of an assembled large 3D structural drug database with associated metabolic and kinetic data. The method will also be extended to predict the effects of SNPs on metabolism.
The MetaCyc Metabolic Pathway Database. Start date: March 2004. Expires: Feb. 2007. Amount: $1,072,879. Principal investigator: Peter Karp. Institution: SRI International. NIH institute: NIGMS.
Proposal to expand the MetaCyc pathway database and the Pathway Tools software used to visualize, query, and edit MetaCyc. Newly discovered pathways and pathways that are diverse among microorganisms and plants, such as secondary metabolism, will be added to the database, and Pathways Tools will be enhanced to include visual displays and internal representations of pathways and chemical compounds, user-querying capabilities, and software-editing capabilities.
Adaptive Methodology for Functional Biomedical Data. Start date: March 2004. Expires: Feb. 2007. Amount: $225,696. Principal investigator: Jeffrey Morris. Institution: University of Texas MD Anderson Cancer Center. NIH institute: NCI.
Researchers plan to develop new Bayesian methodology that provides a unifying framework for performing nonparametric estimation and inference for samples of curves. The methods will be used to model functional data from a series of cancer-related biomedical studies, including colon carcinogenesis studies, an animal study investigating acute renal failure, and medical studies involving proteomics.
Algorithms and Informatics for Analysis of Neural Coding. Start date: March 2004. Expires: February 2008. Amount: $390,102. Principal investigator: Daniel Gardner. Institution: Weill Medical College of Cornell University. NIH institute: NIMH.
Neuroinformatics project that will link four disciplines: experimental neuroscience, analytical computational neuroscience, computer science, and informatics. The project will develop an array of algorithms for neural data analysis that probe how information is represented and processed. The project will design new, parallelized neuroinformatics tools to use with a 26-processor cluster.
Fast Computations for Structural Transitions in Proteins. Start date: April 2004. Expires: March 2009. Amount: $218,179. Principal investigator: Daniel Zuckerman. Institution: University of Pittsburgh. NIH institute: NIGMS.
Project will develop a novel computational approach to study the conformational transitions in the proteins calmodulin, which mediates processes including gene expression, muscle contraction, and mitosis; and myosin, which causes muscle contraction. The new protocol combines residue-level modeling and fine-grid discretization, and has already been used to dynamically simulate dozens of conformational transitions in each of the two 72-residue domains of calmodulin, with “modest computer resources,” according to the grantees.