BindingDB: A Tool for Structure-Based Drug Discovery. Start date: Feb. 2004. Expires: Jan. 2008. Amount: $400,475. Principal investigator: Michael Gilson. Institution: University of Maryland Biotechnology Institute. NIH Institute: NIGMS.
Project to expand the BindingDB database (http://www.bindingdb.org/bind/index.jsp) to allow users to access binding data from the literature in numerical form, and permit querying according to chemical structure.
Optimization of Folding and Threading Proteins. Start date: Feb. 2004. Expires: Jan. 2008. Amount: $238,062. Principal investigator: Ron Elber. Institution: Cornell University, Ithaca. NIH institute: NIGMS.
Project to develop algorithms for predicting protein structures, focusing on bottlenecks such as the folding energy and the ability of making approximate matches. A prediction server at http://ser-loopp.tc.cornell.edu/loopp.html will be updated as the project progresses.
Statistical Methods for Gene Mapping: a New Paradigm. Start date: Jan. 2004. Expires: Dec. 2006. Amount: $147,500. Principal investigator: Shili Lin. Institution: Ohio State University. NIH institute: NHGRI.
Project will develop a set of statistical methods for mapping disease genes for preliminary genome-scan studies. The method will reverse traditional hypotheses for linkage, which usually set the null hypothesis as being no linkage and the alternative hypothesis being linkage.
Continued Support and Development of SBML. Start date: Feb. 2004. Expires: Jan. 2007. Amount: $284,871. Principal investigator: John Doyle. Institution: California Institute of Technology. NIH institute: NIGMS.
Proposal to support and further develop SBML and related software infrastructure. Specific aims include extending the language with new features, maintaining existing software libraries, and producing documentation.
Strategies for Fast Conformational Searching. Start date: Jan. 2004. Expires: Dec. 2006. Amount: $56,308. Principal investigator: Guo-Hong Wu. Institution: University of California, San Francisco. NIH institute: NIGMS.
Supports computational protein folding and docking using the general Convex Global Underestimator (CGU) method, which provides dynamic under-fitting of the energy landscape. The project will combine the general CGU with a physics-based “zipper method” for folding.
Realistic Protein Folding with Hydrophobic Potentials. Start date: March 2004. Expires: Feb. 2007. Amount: $40,320. Principal investigator: Eugene Shakhnovich. Institution: Harvard University. NIH institute: Fogarty International Center.
Project to determine a potential energy function for ab initio folding simulations. An unspecified hydrophobic potential will be combined with a realistic, off-lattice model, with all protein heavy atoms represented explicitly.
Genomic Database for Candida Albicans. Start date: April 2004. Expires: March 2009. Amount: NA. Principal investigator: Gavin Sherlock. Institution: Stanford University. NIH Institute: NIDCR.
Supports development of the Candida Genome Database (CGD), which will contain annotated information about the Candida albicans genome. CGD will reuse the database structures and software developed for the Saccharomyces Genome Database.