ASU Electronic Theses and Dissertations
- 2 English
- 2 Public
Molecular docking serves as an important tool in modeling protein-ligand interactions. Most of the docking approaches treat the protein receptor as rigid and move the ligand in the binding pocket through an energy minimization, which is an incorrect approach as proteins are flexible and undergo conformational changes upon ligand binding. However, modeling receptor backbone flexibility in docking is challenging and computationally expensive due to the large conformational space that needs to be sampled. A novel flexible docking approach called BP-Dock (Backbone Perturbation docking) was developed to overcome this challenge. BP-Dock integrates both backbone and side chain conformational changes of a …
- Bolia, Ashini, Ozkan, Sefika Banu, Ghirlanda, Giovanna, et al.
- Created Date
This study aims to address the deficiencies of the Marcus model of electron transfer (ET) and then provide modifications to the model. A confirmation of the inverted energy gap law, which is the cleanest verification so far, is presented for donor-acceptor complexes. In addition to the macroscopic properties of the solvent, the physical properties of the solvent are incorporated in the model via the microscopic solvation model. For the molecules studied in this dissertation, the rate constant first increases with cooling, in contrast to the prediction of the Arrhenius law, and then decreases at lower temperatures. Additionally, the polarizability of …
- Waskasi, Morteza, Matyushov, Dmitry, Richert, Ranko, et al.
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