Methods development for computational simulation of protein-ligand binding
Abstract/Contents
- Abstract
- Molecular dynamics (MD) simulation offers both high spatial and time resolution into biological processes at an all-atom level, but presents many unique computational challenges in terms of both system setup and compute time. To address the former, I introduce a software package, Dabble, that simplifies system building for MD simulation in a way that supports all commonly used force fields and simulation programs. To increase the accessibility of observing protein-ligand binding in simulations, I developed an adaptive sampling method that guides simulations towards interesting regions of protein-ligand conformational space while requiring no prior knowledge of binding pose or site. Together, these two computational methods improve the ability of researchers to use MD simulation for examining biological processes.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2019; ©2019 |
| Publication date | 2019; 2019 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Betz, Robin |
|---|---|
| Degree supervisor | Dror, Ron, 1975- |
| Thesis advisor | Dror, Ron, 1975- |
| Thesis advisor | Van den Bedem, Henry |
| Thesis advisor | Huang, Possu |
| Thesis advisor | Kobilka, Brian K |
| Degree committee member | Van den Bedem, Henry |
| Degree committee member | Huang, Possu |
| Degree committee member | Kobilka, Brian K |
| Associated with | Stanford University, Department of Biophysics. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Robin Mirdza Betz. |
|---|---|
| Note | Submitted to the Department of Biophysics. |
| Thesis | Thesis Ph.D. Stanford University 2019. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2019 by Robin Betz
- License
- This work is licensed under a Creative Commons Attribution Non Commercial Share Alike 3.0 Unported license (CC BY-NC-SA).
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