Supports improvements for the implicit membrane model (IMM1), which has been implemented into the CHARMM package. Planned improvements include: a more accurate treatment of the solvation free energy of aligned dipoles; an improved treatment of the ionic sidechains incorporating long-range contributions; incorporation of the dipole potential; and implicit solvent modeling of metal ions. New applications will include: prediction and rationalization of the effect of mutations in membrane protein stability; studies of transmembrane helix association; prediction of the membrane binding mode of peripheral membrane proteins; and modeling the membrane insertion mechanism of colicin-type toxins.
NSF Bioinformatics Grants, June 18 — July 27, 2006
Approximate Tandem Repeats Database. Start date: Sept. 1, 2006. Expires: Aug. 31, 2009. Awarded amount to date: $321,308. Principal investigator: Dina Sokol. Sponsor: City University of New York Brooklyn College.
Supports development of a tandem repeat database. The investigators will design an algorithm that finds all tandem repeats within a sequence; implement the algorithm in C++ or Java; design a website, and upload the program as open-source code. The software will be run on the human genome and stored in a database of results.
Computational Prediction of Biological Networks in Microbes and Applications to Cyanobacteria. Start date: Aug. 15, 2006. Expires: July 31, 2007. Awarded amount to date: $363,583. Principal investigator: Ying Xu. Sponsor: University of Georgia Research Foundation.
Supports development of a suite of computational tools for the “elucidation of metabolic and regulatory networks in microbial organisms,” according to the grant abstract. The investigators will use these tools in conjunction with experimental investigation to predict and characterize a number of important metabolic networks and their associated regulatory networks in cyanobacteria. The computational component of the project will rely mainly on information derived through comparative genome analyses and interpretation of microarray gene expression data.
Protein-Ligand Databases in the Lab and Classroom. Start date: Aug. 1, 2006. Expires: July 31, 2009. Awarded amount to date: $452,261. Principal investigator: Heather Carlson. Sponsor: University of Michigan, Ann Arbor.
Supports future development and mining of Binding MOAD (Mother of All Databases, www.BindingMOAD.org), an online database of protein-ligand complexes from the Protein Databank. The investigators will mine the database “to probe the biophysics of molecular recognition,” according to the grant abstract. Areas that will be addressed include the maximum affinity of ligand binding, the degree of burial and packing within a binding site, the role of bridging water molecules, and the contributions of protein flexibility and induced-fit.
Statistical and Computational Methods for the Study of Gene Families. Start date: July 1, 2006. Expires: June 30, 2009. Awarded amount to date: $360,177. Principal investigator: Matthew Hahn. Sponsor: Indiana University.
Funds development of a statistical framework for inferring gene family evolution among species. Goals include the development of improved statistical tools that will “enable more refined estimates of gene duplication and deletion parameters between species, and will provide new ways in which to study gene families within single genomes,” according to the grant abstract. The investigators will also implement a free software package containing these statistical tools.
An Integrated Genomic, Proteomic and Cytological Approach to Understand the Function of Cytoplasmic Localized, Cytoskeletal-Associated RNA-Binding Proteins in Rice. Start date: Sept. 1, 2006. Expires: Aug. 31, 2007. Awarded amount to date: $374,383. Principal investigator: Thomas Okita. Sponsor: Washington State University.
Funds development of a comprehensive, publicly accessible relational database of rice cytoplasmic RNA-binding proteins (http://www.bioinformatics2.wsu.edu/RiceRBP) containing information on their organization into peptide domains, their relationship with orthologous proteins in other plant species, their interacting proteins, their predicted and actual intracellular locations, and their temporal expression patterns. The database will also include raw data including microarrays, 2-D gel maps, and mass spectrometry; lists of molecular tools for biochemical analysis, cytology, and reverse genetics; and laboratory protocols.
MSGR: A Multiple Species Gene Recommender Search Engine for Pathway Discovery. Start date: Aug. 1, 2006. Expires: July 31, 2007. Awarded amount to date: $242,448. Principal investigator: Joshua Stuart. Sponsor: The University of California, Santa Cruz.
Supports development of Multiple Species Gene Recommender, a search engine that scans gene expression datasets across multiple organisms to identify new genes that act in a pathway of interest.
Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB. Start date: July 15, 2006. Expires: June 30, 2007. Awarded amount to date: $960,011. Principal investigator: Volker Brendel. Sponsor: Iowa State University.
Proposal to build PlantGDB (www.plantgdb.org), a cyberinfrastructure portal for plant genomic sequence data. Predicted gene structures will be viewable on dedicated Web-based genome browsers that will enable users to refine existing gene structure annotations and contribute novel ones.
Tailoring Genomic Data to the Needs of Experimental Biologists and Educators. Start date: July 1, 2006. Expires: June 30, 2007. Awarded amount to date: $261,385. Principal investigator: Anton Nekrutenko. Sponsor: Pennsylvania State University Park.
Supports development of a resource that integrates various types of genomic data, including sequences, alignments, and microarray data, with an “extensive array” of analysis tools, according to the grant abstract. The system, called G2, will include a simple interface that would allow instructors to demonstrate principles of genomic biology in school and college classrooms.
Effective Energy Functions for Proteins in Lipid Membranes. Start date: July 1, 2006.
Expires: June 30, 2007. Awarded amount to date: $186,746. Principal investigator: Themis Lazaridis. Sponsor: City University of New York City College.