Computational Studies of the Structure and Biological Activity of Amyloid-Forming Peptides
Start date: Aug. 1, 2010
Expires: July 31, 2011
Awarded amount to date: $78,446
Principal investigator: Jie Zheng
Sponsor: University of Akron
Supports a project that will study the mechanism of toxicity caused by amyloid peptides based on a four-step computational strategy. The project aims to predict amyloid oligomers using an in-house peptide packing program; identify stable amyloid oligomers in solution; determine toxic membrane-bound oligomers and their related mechanism of membrane disruption; and design mutants and ligands to disrupt the formation of stable toxic oligomers.
Exploring Lipid Interactions Using Atomistic Models
Start date: May 1, 2010
Expires: April 30, 2013
Awarded amount to date: $339,996
Principal investigator: Scott Feller
Sponsor: Wabash College
The grantees will use computer simulation methods to study the atomic-level details of interactions within models of cellular membranes. "For example, the interactions between membrane proteins and the phospholipids that constitute the majority of the membrane will be examined with particular interest in how these interactions are determined by the type of lipid," according to the abstract. The team will focus on membranes containing the protein rhodopsin and polyunsaturated phospholipids.
Simulation and Visualization of Biological Systems at Multiple Scales
Start date: March 15, 2010
Expires: Feb. 28, 2011
Awarded amount to date: $95,321
Principal investigator: Joseph Ayoob
Sponsor: University of Pittsburgh
Supports a 10-week training program for 10 students called "Training and Experimentation in Computational Biology," or TECBio. The program will focus on the simulation and visualization of biological systems at multiple scales. "A pool of at least 26 research mentors will provide students with a large array of theoretical and experimental research projects to choose from," the abstract states. "Students will also receive classroom training in topics pertinent to the emerging field of computational biology, such as computational structural biology, cell and systems modeling, computational genomics, and bioimage informatics."
High-Throughput and Multimodality Optical Imaging in Computational Biology
Start date: March 1, 2010
Expires: Feb. 28, 2013
Awarded amount to date: $288,530
Principal investigator: Xiaoyin Xu
Sponsor: Brigham & Women's Hospital
Funds the development of an image database and image analysis toolbox at the Optical Imaging Laboratory at Brigham and Women's Hospital. The database "integrates data obtained from multiple imaging instruments as well as an image processing toolbox implemented using Matlab," according to the grant abstract. The database interacts with the imaging instruments, metadata, and the toolbox and is based on a four-part data model that comprises raw image data, image descriptor data, metadata definitions from image computations, and associated metadata definitions concerning cell line, reagents, experimental subjects, and information from genetics, biology, and experimental design.
Implicit Modeling of Nonpolar Solvation: Towards Reliable Atomistic Simulation of Intrinsically Disordered Proteins
Start date: March 1, 2010
Expires: Feb. 28, 2011 (Estimated)
Awarded amount to date: $111,309
Principal investigator: Jianhan Chen
Sponsor: Kansas State University
Supports a project to improve atomistic simulation of conformational changes in proteins via implicit treatment of the solvent environment. The grantees plan to develop, optimize, and assess novel implicit treatments of nonpolar solvation "to better balance competing electrostatic and nonpolar interactions," according to the abstract. They will also combine simulation and experiment in order to understand the structure, interaction, and control of intrinsically disordered proteins, a class of functional proteins that rely on a lack of stable structures for function.
A Computational Framework for Mapping Ligand Migration Channel Networks and Predicting Molecular Control Mechanisms
Start date: March 1, 2010
Expires: Feb. 29, 2012
Awarded amount to date: $250,000
Principal investigator: Guang Song
Sponsor: Iowa State University
Funds a project to "map the ligand migration channel networks inside proteins and determine the molecular control mechanisms by which these channels are regulated dynamically," according to the grant abstract. As part of this effort, the grantees will develop and employ a computational framework based on the concept of path planning in robotics, because "a ligand's migration in a dynamic protein resembles closely a mobile robot's navigation in a dynamic environment." The proposed approach will integrate geometric mapping with the dynamic exploration of a protein's structure flexibility.
Microbial Genome Annotation Network
Start date: Feb. 15, 2010
Expires: Jan. 31, 2015
Awarded amount to date: $500,000
Principal investigator: Lori Scott
Sponsor: Augustana College
Supports an effort to provide undergraduate students with experience in genome annotation. "Although some parts of this process can be performed with computer-based algorithms, evaluation of those analysis and functional genetic analysis are best performed by researchers," the abstract states. "Those steps provide the opportunity for students to learn and apply current research tools and contribute to a large research effort." The Department of Energy's Joint Genome Institute will provide microbial genome sequence data and training in the use of online annotation tools as part of the project.