| Type of Document |
Master's Thesis |
| Author |
Willcock, Thomas Charles
|
| Author's Email Address |
thomaswillcock@hotmail.com |
| URN |
etd-07142015-171511 |
| Title |
Ligand Docking Benchmark in Rosetta using Explicitly Placed Atomic Orbitals |
| Degree |
Master of Science |
| Department |
Chemistry |
| Advisory Committee |
| Advisor Name |
Title |
| Jens Meiler |
Committee Chair |
| Lidia Smentek |
Committee Member |
| Terry Lybrand |
Committee Member |
|
| Keywords |
- Ligand Docking
- Rosetta
- Score Functions
- Proteins
- Benchmark
- Orbitals
|
| Date of Defense |
2015-08-01 |
| Availability |
unrestricted |
Abstract
Protein-ligand interactions are important in a variety of biological areas. The strength and location of these interactions is driven by Partial Covalent Interactions between the protein and ligand. The Rosetta framework has been updated to explicitly capture and score these interactions. A ligand docking benchmark using this procedure performs between ten and fifteen percent better than the previous procedure performs. Explicit placement of atomic orbitals was used to capture the interactions. Orbitals were placed using hybridization information consistent with quantum chemical calculations performed on the same benchmark set. A statistical model over 8000 high resolution crystal structures was generated in order to score hydrogen bonding interactions, cation-pi interactions, and pi-pi interactions. In most cases, important binding interactions were captured.
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| Files |
| Filename |
Size |
Approximate Download Time
(Hours:Minutes:Seconds)
|
| 28.8 Modem |
56K Modem |
ISDN (64 Kb) |
ISDN (128 Kb) |
Higher-speed Access |
| |
Willcock.pdf |
2.75 Mb |
00:12:43 |
00:06:32 |
00:05:43 |
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00:00:14 |
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