Multi-Resolution Docking Methods for Electron Microscopy

University Of Texas Hlth Sci Ctr Houston, Houston TX

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Abstract

DESCRIPTION (provided by applicant): Macromolecular assemblies are the basic functional units of biological cells;they furnish targets for drug design, as deficiencies in their architecture are frequently linked to health problems. The overall goal of the proposed research is the development of computational quantitative fitting tools for electron microscopy (EM) that combine low-resolution image reconstructions of large assemblies with complementary atomic resolution data of individual subunits for routine determination of the large-scale structure of biomolecular machines. Key questions to be addressed include: (i) How can one accurately identify geometric features of structural data that may serve as anchor points for rigid body and flexible matching? (ii) How can one take into account the conformational variability (heterogeneity) of molecular structures in the design of matching algorithms? (iii) Is a six-dimensional rigid-body search based on the classical cross-correlation coefficient sufficiently efficient for a real-time alignment of structures? (iv) How can one best disseminate our innovations to the global user community in the form of free open source software packages? We will use reduced models from pattern matching and neural networks for a coarse estimation of density maps and for determining suitable landmarks for the registration of multi-resolution data. Complementary to this indirect approach an exhaustive rigid body search will be performed in reciprocal space using parallel computing architectures (for computational speed) based in part on the correlation of the compared data sets (for accuracy). A computational laboratory supported by this project will be used extensively for software development and for fitting applications in EM. Collaborative efforts will include the refinement of myosin motors, GroEL chaperonins, and RNA polymerase assemblies. The results of these developments will be new computer codes that provide a comprehensible and flexible approach to the multi-resolution modeling of large assemblies. The algorithmic and methodological developments will be distributed freely through the established internet-based mechanisms employed for the Situs docking package.