ITR: Subnanometer Structure Based Fold Determination of Biological Complex

University Of California-San Francisco, San Francisco CA

Investigators

Abstract

EIA-0325550 University of Texas Chandrajit L. Bajaj COLLABORATIVES: ITR: Subnanometer Structure Based Fold Determination of Biological Complexes . We propose to form a team of three independent investigators with different expertises to co-develop the necessary computation and visualization methodology for biologists to quickly, easily and accurately deduce the folds of the domain components of large macromolecular complexes. While structures of macromolecular complexes are becoming more prevalent, and the size of some density maps would increase up to 1GB, the visualization and analysis requirements to extract important biological information are far beyond the currently available software. Our research task will explore different algorithms to enhance the signal through denoising of the 3-dimensional structure, visualize these large and filtered maps effectively, extract the individual protein components and their salient structural features such as a helices and b sheets accurately, and ultimately construct pseudo atomic model with novel structure prediction methods using protein sequence and structure considerations as constraints. We will set up a test data set, comprised of both simulated and experimental structures, to validate each of our development steps. The software developments in each of the research sites will be glued together using a scripting language (Python) and made easy to use through a graphical interface. Additionally, the software will be extensively documented and distributed via an open source policy, encouraging continued collaboration and development.