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Title page for ETD etd-07142015-171511


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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