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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Apr 14, 2003


Computational Mapping of Proteins for Binding of Ligands. Start date: Feb. 2003. Expires Jan. 2007. Amount: $216,624. Principal investigator: Sandor Vajda. Institution: Boston University. NIH Institute: NIGMS.

Project aims to develop software for high-throughput computational solvent mapping — a method that places molecular probes on a protein surface to predict the most favorable binding positions. Solvent mapping will also be tested for its ability to identify functional sites in other types of proteins.


Computer Modeling of Biomolecular Systems. Start date: March 2003. Expires: Nov. 2003. Amount: $100,000. Principal Investigator: James Stewart. Institution: Stewart Computational Chemistry. NIH Institute: NIGMS.

Project will develop software for full quantum mechanics modeling of biological macromolecules. The software will be based on a semi-empirical quantum chemical compute engine with a newly developed parameterization for all biological elements. Phase I will determine whether an accuracy of 3 kcal/mol can be achieved for biological systems.


Computational and Experimental Tool for Cancer Protein. Start date: March 2003. Expires: Feb. 2005. Amount: $52,580. Principal Investigator: Keith Dunker. Institution: Molecular Kinetics. NIH Institute: NCI.

Based on previous work that used proprietary PONDR (Predictors of Natural Disordered Regions) software to reveal that a set of oncogenes is likely to contain significantly more disorders than other protein types, project will create a database called “Cancer DisProt” that contains correlations of disorder/order with cancer-associated protein function.


Evolutionary Computation for Gene Expression Analysis. Start Date: April 2003. Expires: Sept. 2003. Amount: $99,956. Principal Investigator: Gary Fogel. Institution: Natural Selection. NIH Institute: NCI.

Supports development of software that can classify cancers using gene expression profiling. Project will train and design multi-layer feed-forward and artificial neural networks using evolutionary optimization techniques for cancer cell class prediction and discovery.


Single-Molecule Image Analysis for DNA Sequencing. Start date: April 2003. Expires: Sept. 2003. Amount: $117,150. Principal Investigator: Patrick Humphrey. Institution: Li-Cor. NIH Institute: NHGRI.

Supports development of a system for real-time single-molecule DNA sequencing based on “charge-switched” nucleotides, an adapted DNA polymerase, a method for isolating and handling single DNA molecules, a microfluidics flowcell for sorting molecules by charge, a total internal reflection optical system for single-molecule detection in four spectral channels, and software algorithms for single-molecule detection and system control. Project will also develop data analysis techniques and algorithms to perform single-molecule base-calling charge-coupled-device images.


Database Software for Complex Cell Biological Pathways. Start Date: April 2003. Expires: March 2004. Amount: $99,700. Principal Investigator: Robert Phair. Institution: Integrative Bioinformatics. NIH Institute: NIGMS.

Phase I SBIR grant supports development of a software platform called ProcessDB that integrates database technology and kinetic modeling to support the formulation, quantification, comparison, and testing of cellular models. A database of molecular biology objects, including molecules, complexes, cellular locations, states, and processes, will enable cell biologists to translate and export their diagrams, hypotheses, and experimental protocols to third-party modeling and optimization software for simulation and parameter estimation.


Facility Core 3 - Biocomputing and Bioinformatics. Start date: April 2003. Expires: March 2007. Principal Investigator: Richard Larson. Institution: University of New Mexico Albuquerque. NIH Institute: NIEHS.

Supports a biocomputing and bioinformatics core facility for the New Mexico Environmental Health Sciences Center, which will study gene and environmental factor interactions as well as the influence of socio-economic status and behavioral issues on environmental disease.

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