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.
| Identifer | oai:union.ndltd.org:VANDERBILT/oai:VANDERBILTETD:etd-03182013-141442 |
| Date | 08 April 2013 |
| Creators | Putnam, Daniel Kent |
| Contributors | Jens Meiler, Terry Lybrand, David Tabb |
| Publisher | VANDERBILT |
| Source Sets | Vanderbilt University Theses |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.library.vanderbilt.edu/available/etd-03182013-141442/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Vanderbilt University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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