<p> Computational modeling of RNA-protein interactions remains an important endeavor. However, exclusively all-atom approaches that model RNA-protein interactions via molecular dynamics are often problematic in their application. One possible alternative is the implementation of hierarchical approaches, first efficiently exploring configurational space with a coarse-grained representation of the RNA and protein. Subsequently, the lowest energy set of such coarse-grained models can be used as scaffolds for all-atom placements, a standard method in modeling protein 3D-structure. However, the coarse-grained modeling likely will require improved ribonucleotide-amino acid potentials as applied to coarse-grained structures. As a first step we downloaded 1,345 PDB files and clustered them with PISCES to obtain a non-redundant complex data set. The contacts were divided into nine types with DSSR according to the 3D structure of RNA and then 9 sets of potentials were calculated. The potentials were applied to score fifty thousand poses generated by FTDock for twenty-one standard RNA-protein complexes. The results compare favorably to existing RNA-protein potentials. Future research will optimize and test such combined potentials. </p>
| Identifer | oai:union.ndltd.org:PROQUEST/oai:pqdtoai.proquest.com:10241445 |
| Date | 11 February 2017 |
| Creators | Kimura, Takayuki |
| Publisher | San Jose State University |
| Source Sets | ProQuest.com |
| Language | English |
| Detected Language | English |
| Type | thesis |
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