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Title page for ETD etd-03182013-141442


Type of Document Master's Thesis
Author Putnam, Daniel Kent
Author's Email Address daniel.k.putnam@vanderbilt.edu
URN etd-03182013-141442
Title BCL::SAXS - Small Angle X-Ray Scattering Profiles to Assist Protein Structure Prediction
Degree Master of Science
Department Biomedical Informatics
Advisory Committee
Advisor Name Title
Jens Meiler Committee Chair
David Tabb Committee Member
Terry Lybrand Committee Member
Keywords
  • BCL::Fold
  • CRYSOL
  • de novo protein structure determination
  • Debye formula
  • GPU Acceleration
  • small angle X-ray scattering
Date of Defense 2013-01-14
Availability unrestricted
Abstract
The Biochemical Library (BCL) is a protein structure prediction algorithm developed in the Meiler Lab at Vanderbilt University based on the placement of secondary structure elements. This algorithm can use experimental data such as nuclear magnetic resonance (NMR), Cryo-electron microscopy (CryoEM), and electron paramagnetic resonance (EPR), to assist in protein structure prediction but does not have the ability to use SAXS data. The first phase of my project was to add this capability to the BCL and create a SAXS compatibility score. GPU acceleration was used to parallelize the computations. The second phase of the project was to compute SAXS scores for protein models without side chain and loop region coordinate information, but preserve atom type information. Finally, the BCL::SAXS score was added to the minimization process in BCL::FOLD. The SAXS score can be used to filter erroneous initial protein models from further refinement, thus saving time and computation resources.
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